Genes associated with the maintenance of differentiation of smooth muscle cells

ABSTRACT

A cDNA fragment participating in the maintenance of smooth muscle differentiation was isolated using a culture system of chicken gizzard smooth muscle cells, the differential display method and the subtracted hybridization method. Using the obtained cDNA sequence as a query, cDNA sequences of Helix Research Institute (Japanese Patent Application No. 2000-118776) were retrieved, and thus, a novel gene “C-NT2RP3001495” was obtained. The protein encoded by this gene has two WW domains that participate in protein interactions in the N-terminal domain. Evidence suggests that this protein binds to other proteins, and thus regulates the intracellular signal transduction, gene expression, and so on, thereby participating in the maintenance of the differentiation of smooth muscle cells. This protein and compounds regulating the expression thereof are markedly useful in developing drugs for various diseases associated with abnormality in the maintenance of smooth muscle cell differentiation.

RELATED APPLICATIONS

This application is a divisional application of U.S. patent applicationSer. No. 10/058,518, filed Jan. 28, 2002, now U.S. Pat. No. 6,908,748;which is a continuation-in-part of PCT/JP00/05059, filed Jul. 28, 2000,which claims priority to U.S. Provisional Application Nos. 60/159,590,filed Oct. 18, 1999, and 60/183,322, filed Feb. 17, 2000; and JapanesePatent Application Nos. 11-248036, filed Jul. 29, 1999; 2000-118776,filed Jan. 11, 2000; and 2000-183767, filed May 2, 2000. The entiredisclosure of each of the above applications is hereby incorporated byreference.

TECHNICAL FIELD

The present invention relates to novel human proteins associated withthe maintenance of differentiation of smooth muscle cells.

BACKGROUND

The smooth muscle cell is a major muscle cell in tissues such as bloodvessel, trachea, digestive tract, urinary bladder, and uterus, and itsimportant function is the regulation of contraction and relaxation.Recently, a relationship has been revealed between phenotypic modulationof the smooth muscle cells, wherein the cell looses the contractionability and thereby acquires proliferation ability, and the pathologicalstate. The proliferation of vascular smooth muscle cell is closelyassociated with the manifestation of the pathological state such asrestenosis occurring after percutaneous transluminal coronaryangioplasty (PTCA). It has been clarified that vascular tunica mediasmooth muscle cells acquire motility through phenotypic modulation to adedifferentiated type in the early stage of the onset ofarteriosclerosis, and thus, migrate to the vascular endothelium, whichis the major cause of hypertrophy of vascular endothelium. However,there are still many obscure points about the phenotypic modulation ofsmooth muscle cells, for example, associated genes, molecular mechanismthereof, and so on. A better understanding of how the smooth musclecells maintain the differentiated phenotype and how their phenotypes areconverted to the dedifferentiated type is needed to develop therapeuticmethods for morbid states caused by smooth muscle cell proliferation.The mechanism of the phenotypic modulation may be elucidated byanalyzing the genes associated with the maintenance of differentiatedtype of smooth muscle cells, such genes being applicable as therapeuticagents and diagnostic agents for diseases caused by the aberrantproliferation of smooth muscle cells; ischemic heart diseases such asarteriosclerosis, myocardial infarction, aortic aneurysm, and cerebralapoplexy; cerebral vascular disorders; and vascular dementia. Inaddition, glomerulonephritis, pulmonary fibrosis, cerebral,arteriosclerosis, and hepatitis, which correspond to a state of aberrantproliferation of mesangial cells, alveolar epithelial cells, pericytes,and lto cells, respectively—cells that have extremely similarcharacteristics to the smooth muscle cells—are presumed to be diseasescaused by cellular transformation occurring through a mechanism similarto that of smooth muscle cells; and thus, the genes therein may also beapplicable as therapeutic agent and diagnostic agent for these chronicdiseases.

SUMMARY

The object of the present invention is to provide novel proteinsassociated in the maintenance of differentiation of smooth muscle cells,genes encoding them, and production and use of the proteins and genes.

To accomplish the objects described above, the present inventorsvigorously carried out the following research. The present inventorsfirst constructed a cDNA library by subtracting cDNAs ofdedifferentiated smooth muscle cells derived from chicken gizzard fromcDNAs of differentiated smooth muscle cells derived from chickengizzard, in order to elucidate the mechanism for the maintenance ofdifferentiation of smooth muscle cells. The nucleotide sequence of theobtained cDNA fragment was determined, and thus a sequence (SEQ ID NO:3)named “12F08” was obtained. It has been revealed that “12F08” exhibits ahomology of 82% to the clone Hs#S1388556 belonging to a human Unigenecluster Hs.128045.

In the next step, the present inventors obtained the“Hs128045_(—)12F08con” sequence by preparing a contig via assemblingsequences belonging to the human Unigene cluster Hs.128045. The pfammotif database was then searched for the “Hs128045_(—)12F08con” byutilizing estwisedb in the database search program Wise2 designed byEwan Birney at Sanger Center. The results showed that each of 12F08 andHs128045_(—)12F08con contained two WW domains that are importantfunctional domains for protein-protein interaction.

Furthermore, the present inventors searched cDNA sequences of HelixResearch Institute (helix clones; Japanese Patent Application No. Hei11-248036; Japanese Patent Application No. 2000-118776) for homologuesusing the above-mentioned sequence, “Hs 128045_(—)12F08con”, obtainedfrom Unigene Cluster as a query. These helix clones are highly expectedto have the full length sequence, which are obtained by the combined useof: [1] preparation of cDNA library, which comprises cDNA having afull-length sequence at a high rate, by the oligo-capping method; and[2] evaluation system for the cDNA to determine whether it contains thefull-length sequence based on the 5′ end sequence (the selection isachieved based on the evaluation using ATGpr after eliminating non-fulllength clones as compared with an EST). The results of homology searchshowed that the query clone was identical to the helix clone“C-NT2RP3001495”. In addition, it was also revealed that the query cloneis identical to the gene for Hs.519 Human oxidoreductase (HHCMA56) ofUnigene. However, the sequence of HHCMA56 contains reading mistakes ofnucleotides, and thus it has been deposited as a gene encoding a proteinconsisting of 371 amino acids which is entirely different from theprotein of “C-NT2RP3001495”. Thus, it can be stated that“C-NT2RP3001495” is a novel protein found for the first time by thepresent inventors. The “C-NT2RP3001495” is a protein consisting of 414amino acids, which has two WW domain sequences.

The present inventors then analyzed the expression level of gene “12F08”in a variety of tissues by real-time PCR. The results showed that thegene was expressed at high levels in the differentiated smooth muscleand gizzard, suggesting that “12F08” encodes a protein associated withthe maintenance of differentiation of smooth muscle cells. Thus, human“C-NT2RP3001495” is presumed to be a protein associated with themaintenance of differentiation of smooth muscle cells.

The human “C-NT2RP3001495” is expected to be useful as a pharmaceuticalfor diseases caused by the aberrant proliferation of smooth musclecells; ischemic heart diseases such as arteriosclerosis, myocardialinfarction, aortic aneurysm, cerebral apoplexy; cerebral vasculardisorders; and vascular dementia; as well as for glomerulonephritis,pulmonary fibrosis, cerebral arteriosclerosis, and hepatitis, whichcorrespond to the states of aberrant proliferation of mesangial cells,alveolar epithelial cells, pericytes, and lto cells, respectively—cellswhich have extremely similar characteristics to the smooth muscle cells.

As described above, the present inventors found novel proteinsassociated with the maintenance of differentiation of smooth musclecells, and thereby accomplished the present invention.

Specifically, the present invention relates to novel proteins whichparticipate in the maintenance of differentiation of smooth musclecells, genes encoding the proteins, and production and uses of theproteins and genes. More specifically, the present invention providesthe following:

[1] a DNA of any one of the following (a) to (d):

(a) a DNA encoding a protein consisting of the amino acid sequence ofSEQ ID NO:2,

(b) a DNA comprising the coding region of the nucleotide sequence of SEQID NO:1,

(c) a DNA encoding a protein which (i) comprises the amino acid sequenceof SEQ ID NO:2 in which one or more amino acids are substituted,deleted, inserted and/or added, and (ii) is functionally equivalent tothe protein consisting of the amino acid sequence of SEQ ID NO:2, and

(d) a DNA hybridizing under a stringent condition to a DNA consisting ofthe nucleotide sequence of SEQ ID NO:1, which encodes a proteinfunctionally equivalent to the protein consisting of the amino acidsequence of SEQ ID NO:2;

[2] a DNA encoding a partial peptide of a protein consisting of theamino acid sequence of SEQ ID NO:2;

[3] a protein or peptide encoded by the DNA of [1] or [2];

[4] a vector into which the DNA of [1] or [2] has been inserted;

[5] a host cell containing the DNA of [1] or [2], or the vector of [4];

[6] a method for producing the protein or peptide of [3], whichcomprises the steps of culturing the host cell of [5], and recoveringthe expressed protein from the host cell or the culture supernatant;

[7] an antibody binding to the protein of [3];

[8] a polynucleotide containing at least 15 nucleotides complementary toa DNA consisting of the nucleotide sequence of SEQ ID NO:1 or thecomplementary strand thereof; and

[9] a method of screening for a compound that binds to the protein of[3], which comprises the steps of:

(a) contacting a test sample containing at least one compound with theprotein or a partial peptide thereof,

(b) detecting the binding activity of the compound with the protein or apartial peptide thereof, and

(c) selecting the compound that has the activity of binding to theprotein or a partial peptide thereof.

The present invention provides a human-derived gene “C-NT2RP3001495”that encodes a novel protein which participates in the maintenance ofdifferentiation of smooth muscle cells. The nucleotide sequence ofhuman-derived cDNA “C-NT2RP3001495” is shown in SEQ ID NO:1, and theamino acid sequence encoded by the cDNA is shown in SEQ ID NO:2. As seenin SEQ ID NO:1, the human cDNA “C-NT2RP3001495” has an ORF encoding aprotein consisting of 414 amino acids.

The inventive human “C-NT2RP3001495” gene has been selected as a helixclone (Japanese Patent Application No. Hei 11-248036; Japanese PatentApplication No. 2000-118776) exhibiting homology to the cDNA fragment“12F08”, isolated as a gene fragment associated with the maintenance ofsmooth muscle differentiation by using culture system of chicken gizzardsmooth muscle cells. High expression of the above-mentioned “12F08” wasobserved in differentiated smooth muscle and gizzard. Further, theresults of a motif search showed that the protein contained two WWdomains in the N-terminal region that participate in protein-proteininteraction. This suggests that the protein binds to other proteins andregulates intracellular signal transduction, gene expression or thelike, and thereby participates in the maintenance of differentiation ofsmooth muscle cells. Further, the human “C-NT2RP3001495” protein of thepresent invention has an Adh short motif that is found inoxidoreductases and dehydrases, and therefore, it is potentially anoxidoreductase or dehydrase itself.

The expression pattern and structural properties of human“C-NT2RP3001495” suggest that it serves an important function in livingbody, and thus, it can be a useful target for drug development. Inaddition, compounds binding to human “C-NT2RP3001495” and compoundsregulating human “C-NT2RP3001495” gene expression are expected to beapplicable for the development of prophylactic or therapeutic agents fora variety of diseases caused by abnormalities in the maintenance ofdifferentiation of smooth muscle cells.

Further the present invention includes proteins functionally equivalentto the human “C-NT2RP3001495” protein (SEQ ID NO:2). Such proteinsinclude, for example, mutants, homologues, and variants of the human“C-NT2RP3001495” protein. The term “functionally equivalent” hereinmeans that the protein of interest has a function associated with themaintenance of differentiation of smooth muscle cells like that of the“C-NT2RP3001495” protein. Specifically, the smooth muscle cells can bedivided into two types, namely differentiated and dedifferentiated typesthereof, by utilizing the expression of genes, such as the expression ofcalponin gene or h-caldesmon gene, which are characteristic ofregulations at the transcription level and at the mRNA splicing levelthat are known as characteristics of the differentiated state (CellTechnology, 16(10):1496 (1997)). The levels of gene expression arecompared between the differentiated cells and dedifferentiated cellsprepared from the smooth muscle cells in which genes characteristic ofthe differentiated type are expressed. When the expression level of agene is significantly higher or alternatively lower in thedifferentiated smooth muscle cells than in dedifferentiated cells, thenit can be determined that it is highly probable that the gene has afunction associated with the maintenance of differentiation. Forexample, chicken gizzard smooth muscle cells are included in smoothmuscle cells in which genes characteristic of the differentiated typeare expressed.

One method for preparing functionally equivalent proteins well known tothose skilled in the art involves the introduction of mutations into theproteins. For example, one skilled in the art can prepare proteinsfunctionally equivalent to the human “C-NT2RP3001495” protein (SEQ IDNO:2) by introducing appropriate mutations into the amino acid sequenceof the protein using the site-directed mutagenesis method(Hashimoto-Gotoh, et al., Gene 152:271-275, 1995; Zoller et al., MethodsEnzymol. 100:468-500, 1983; Kramer, et al., Nucleic Acids Res.12:9441-9456, 1984; Kramer et al., Methods. Enzymol. 154:350-367, 1987;Kunkel, Proc. Natl. Acad. Sci. USA. 82:488-492, 1985; Kunkel, MethodsEnzymol. 85:2763-2766, 1988) and such. Mutation of amino acids may occurin nature, too. The proteins of the present invention include proteinscomprising the amino acid sequence of human “C-NT2RP3001495” protein(SEQ ID NO:2) in which one or more amino acids are mutated, so long asthe resulting mutant protein is functionally equivalent to the protein.In such a mutant protein, the number of the amino acids to be mutated isusually 50 residues or less, preferably 30 residues or less, and morepreferably 10 residues or less (e.g., 5 residues or less).

The amino acid residue to be mutated is preferably mutated into adifferent amino acid that allows the properties of the amino acidside-chain to be conserved. Examples of properties of amino acid sidechains include: hydrophobic amino acids (A, I, L, M, F, P, W, Y, V),hydrophilic amino acids (R, D, N, C, E, Q, G, H, K, S, T), and aminoacids comprising the following side chains: an aliphatic side-chain (G,A, V, L, I, P); a hydroxyl group containing side-chain (S, T, Y); asulfur atom containing side-chain (C, M); a carboxylic acid and amidecontaining side-chain (D, N, E, Q); a base containing side-chain (R, K,H); and an aromatic containing side-chain (H, F, Y, W) (The parentheticletters indicate the one-letter codes of amino acids).

It is well known that a protein having deletion, addition, and/orsubstitution of one or more amino acid residues in the sequence of aprotein can retain the original biological activity (Mark et al.; Proc.Natl. Acad. Sci. U.S.A. 81:5662-5666, 1984; Zoller et al., Nucleic AcidsRes. 10:6487-6500, 1982; Wang et al., Science 224:1431-1433;Dalbadie-McFarland et al. Proc. Natl. Acad. Sci. U.S.A. 79:6409-6413,1982).

A protein having the amino acid sequence of human “C-NT2RP3001495”protein to which one or more amino acid residues have been added, isexemplified by a fusion protein containing the human “C-NT2RP3001495”protein. Fusion proteins, in which the human “C-NT2RP3001495” protein isfused to other peptides or proteins, are included in the presentinvention. Fusion proteins can be made using techniques well known tothose skilled in the art, for example, by linking the DNA encoding thehuman “C-NT2RP3001495” protein (SEQ ID NO:2) in frame with the DNAencoding other peptides or proteins, followed by inserting the DNA intoan expression vector and expressing it in a host. There is norestriction as to the peptides or proteins to be fused to the protein ofthe present invention.

For instance, known peptides which may be used for the fusion includethe FLAG peptide (Hopp et al., Biotechnology 6:1204-1210, 1988), 6×Histhat is made up of six histidine residues, 10×His, influenzahemagglutinin (HA), human c-myc fragment, VSV-GP fragment, p18HIVfragment, T7-tag, HSV-tag, E-tag, SV40 T antigen fragment, lck tag,α-tubulin fragment, B-tag, and Protein C fragment. Also,glutathione-S-transferase (GST), influenza hemagglutinin (HA), theconstant region of immunoglobulin, β-galactosidase, maltose bindingprotein (MBP), and the like may be used as a protein to be fused withthe protein of this invention. Fusion proteins can be prepared by fusingthe DNA encoding these peptides or proteins, which are commerciallyavailable, with the DNA encoding the protein of the invention, andexpressing the fused DNA.

An alternative method for preparing functionally equivalent proteinsknown to those skilled in the art utilizes, for example, thehybridization technique (Sambrook et al., Molecular Cloning 2nd ed.9.47-9.58, Cold Spring Harbor Lab. Press, 1989). Generally, one skilledin the art can isolate DNAs highly homologous to the whole or part ofthe DNA sequence encoding the human “C-NT2RP3001495” protein (SEQ IDNO:1), and then isolate proteins functionally equivalent to the human“C-NT2RP3001495” protein based on those DNAs isolated. The presentinvention includes proteins that are (i) encoded by a DNA hybridizing toa DNA encoding the protein of human “C-NT2RP3001495” and (ii)functionally equivalent to the human protein of “C-NT2RP3001495”. Suchproteins include, for example, homologues derived from human and otheranimals (for example, protein encoded by a DNA from mouse, rat, rabbit,cattle, chicken, etc.). The protein (SEQ ID NO:4) encoded by “12F08” maybe exemplified as the homologue from chicken.

Those skilled in the art can properly select hybridization conditions tobe used for the isolation of DNAs encoding proteins functionallyequivalent to the human protein of “C-NT2RP3001495”. Hybridizationconditions include low stringent conditions. Low stringent conditionsmay be, for example, 42° C. in 2×SSC and 0.1% SDS, preferably 50° C. in2×SSC and 0.1% SDS for washing after hybridization. More preferably,high stringent conditions such as 65° C. in 0.1×SSC and 0.1% SDS may bechosen. DNA with higher homology may be efficiently obtained at highertemperature under these conditions. However, several factors are thoughtto influence the stringency of hybridization, such as temperatures andsalt concentrations, and one skilled in the art can suitably selectthese factors to accomplish a similar stringency. More guidelines forthe hybridization condition are available in the art, for example, in areference by Sambrook et al. (1989, Molecular Cloning, A LaboratoryManual, Cold Spring Harbor Press, N.Y.) and in unit 2.10 of thereference by Ausubel et al. (1995, Current Protocols in MolecularBiology, John Wiley & Sons, N.Y.).

Also, in lieu of hybridization, it is also possible to isolatefunctionally equivalent proteins by a gene amplification method, such asPCR, by synthesizing sequences based on the sequence information of theDNA encoding the human “C-NT2RP3001495” protein (SEQ ID NO:1) and usingthem as primers.

The proteins functionally equivalent to the human “C-NT2RP3001495”proteins encoded by the DNA isolated by the hybridization or geneamplification techniques, usually are highly homologous to the human“C-NT2RP3001495” proteins (SEQ ID NO:2) at the amino acid sequencelevel. The proteins of the invention include proteins functionallyequivalent to the human “C-NT2RP3001495” protein and are highlyhomologous to the amino acid sequence of SEQ ID NO:2. “Highlyhomologous” means typically 65% or higher, preferably 75% or higher,more preferably 85% or higher, and even more preferably 95% or higheridentity at the amino acid level. Homology between proteins can bedetermined according to the algorithm described in the literature(Wilbur et al., Proc. Natl. Acad. Sci. USA 80:726-730, 1983).

The proteins of the present invention may have variations in the aminoacid sequence, molecular weight, isoelectric point, presence or absenceof sugar chains, or form, depending on the cell or host used to producethem or the purification method utilized as described below.Nevertheless, so long as the protein obtained has a function equivalentto the human “C-NT2RP3001495” protein, it is within the scope of thepresent invention. For example, when the inventive protein is expressedin prokaryotic cells, e.g., E. coli, a methionine residue is added atthe N-terminus of the original protein. The present invention alsoincludes such proteins.

The proteins of the present invention can be prepared as recombinantproteins or as naturally occurring proteins, using methods commonlyknown in the art. The recombinant protein can be, for example, preparedas follows. The DNA encoding the protein of this invention (e.g., DNAhaving the nucleotide sequence of SEQ ID NO:1) is inserted into anappropriate expression vector, and introduced into suitable host cells.Subsequently, the resulting transformants, the host cell inserted withthe expression vector, are recovered, extracted and then purified bychromatography utilizing ion exchange, reverse phase, or gel filtration,or by affinity chromatography with a column in which the antibodiesagainst the protein of the present invention are fixed, or by acombination of these columns.

Alternatively, the protein of the invention can be prepared byexpressing the protein in host cells (e.g., animal cells or E. coli) asa fusion protein with glutathione S transferase protein, or as arecombinant protein with multiple histidine residues. The expressedprotein can be purified using a glutathione column or nickel column.Subsequently, if necessary, regions of the fusion protein (apart fromthe desired protein) can be digested and removed with thrombin, factorXa, etc.

The natural protein corresponding to the protein of the invention can beisolated by methods well known in the art, for example, by purifyingtissue or cell extracts containing a protein of the invention with anaffinity column to which the antibody that binds to the protein of thepresent invention described below is bound. The antibody may be apolyclonal antibody or monoclonal antibody.

The term “substantially pure” as used herein in reference to a givenpolypeptide means that the polypeptide is substantially free from otherbiological macromolecules. For example, the substantially purepolypeptide is at least 75%, 80, 85, 95, or 99% pure by dry weight.Purity can be measured by any appropriate standard method known in theart, for example, by column chromatography, polyacrylamide gelelectrophoresis, or HPLC analysis.

Accordingly, the invention includes a polypeptide having a sequenceshown as SEQ ID NO:2. The invention also includes a polypeptide, orfragment thereof, that differs from the corresponding sequence shown asSEQ ID NO:2. The differences are, preferably, differences or changes ata non-essential residue or a conservative substitution. In oneembodiment, the polypeptide includes an amino acid sequence at leastabout 60% identical to a sequence shown as SEQ ID NO:2, or a fragmentthereof. Preferably, the polypeptide is at least 65%, 70%, 75%, 80%,85%, 90%, 95%, 98%, 99% or more identical to SEQ ID NO:2 and has atleast one cell differentiation-related function or activity describedherein, e.g., the polypeptide is involved in the maintenance ofdifferentiation of smooth muscle cells. Preferred polypeptide fragmentsof the invention are at least 10%, preferably at least 20%, 30%, 40%,50%, 60%, 70%, or more, of the length of the sequence shown as SEQ IDNO:2 and have at least one cell differentiation-related function oractivity described herein. Alternatively, the fragment can be merely animmunogenic fragment.

The present invention also includes partial peptides of the proteins ofthe present invention. The partial peptides of the present inventioncomprise at least 7 or more amino acids, preferably 8 or more aminoacids, more preferably 9 or more amino acids. The partial peptides canbe used, for example, for generating antibodies against the protein ofthe present invention, screening of compounds binding to the protein ofthe present invention, or screening of promoters or inhibitors for theprotein of the present invention. The partial peptides can be used asantagonists or competitive inhibitors for the protein of this invention.The partial peptides of the invention can be produced by geneticengineering, known methods of peptide synthesis, or by digesting theprotein of the invention with an appropriate peptidase. For peptidesynthesis, for example, solid phase synthesis or liquid phase synthesismay be used.

DNA encoding an inventive protein can be used for the production of theinventive protein in vivo and in vitro as described above: it is alsoapplicable to, for example, gene therapy for diseases caused by theabnormality in the gene encoding the inventive protein and for diseasesthat can be treated by the inventive protein. Any type of DNA, such ascDNA synthesized from mRNA, genomic DNA or synthetic DNA, can be used solong as the DNA encodes a protein of the present invention. Also so longas they can encode a protein of the present invention, DNAs comprisingarbitrary sequences based on the degeneracy of the genetic code are alsoincluded.

The DNA of the present invention can be prepared using methods known inthe art. For example, a cDNA library can be constructed from the cellsexpressing the protein of the present invention, and hybridization canbe conducted using a part of the DNA sequence of the present invention(for example, SEQ ID NO:1) as a probe, cDNA libraries may be preparedby, for example, the method described in the literature (Sambrook etal., Molecular Cloning, Cold Spring Harbor Laboratory Press, 1989), andalso, commercially available ones can be used. Alternatively, the DNA ofthe present invention can be obtained by preparing the RNA from thecells expressing the protein of the present invention, synthesizing cDNAby reverse transcriptase, synthesizing the oligo-DNAs based on the DNAsequence of the present invention (for example, SEQ ID NO:1), andamplifying the cDNA encoding the protein of the present invention by PCRusing the oligonucleotides as primers.

As used herein, an “isolated nucleic acid” is a nucleic acid, thestructure of which is not identical to that of any naturally occurringnucleic acid or to that of any fragment of a naturally occurring genomicnucleic acid spanning more than three genes. The term therefore covers,for example, (a) a DNA which has the sequence of part of a naturallyoccurring genomic DNA molecule but is not flanked by both of the codingsequences that flank that part of the molecule in the genome of theorganism in which it naturally occurs; (b) a nucleic acid incorporatedinto a vector or into the genomic DNA of a prokaryote or eukaryote in amanner such that the resulting molecule is not identical to anynaturally occurring vector or genomic DNA; (c) a separate molecule suchas a cDNA, a genomic fragment, a fragment produced by polymerase chainreaction (PCR), or a restriction fragment; and (d) a recombinantnucleotide sequence that is part of a hybrid gene, i.e., a gene encodinga fusion protein. Specifically excluded from this definition are nucleicacids present in random, uncharacterized mixtures of different DNAmolecules, transfected cells, or cell clones. e.g., as these occur in aDNA library such as a cDNA or genomic DNA library.

Accordingly, in one aspect, the invention provides an isolated orpurified nucleic acid molecule that encodes a polypeptide describedherein or a fragment thereof. Preferably, the isolated nucleic acidmolecule includes a nucleotide sequence that is at least 60% identicalto the nucleotide sequence shown in SEQ ID NO:1. More preferably, theisolated nucleic acid molecule is at least 65%, 70%, 75%, 80%, 85%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, identical to thenucleotide sequence shown in SEQ ID NO:1. In the case of an isolatednucleic acid molecule which is longer than or equivalent in length tothe reference sequence, e.g., SEQ ID NO:1, the comparison is made withthe full length of the reference sequence. Where the isolated nucleicacid molecule is shorter that the reference sequence, e.g., shorter thanSEQ ID NO:1, the comparison is made to a segment of the referencesequence of the same length (excluding any loop required by the homologycalculation).

As used herein. “% identity” of two amino acid sequences, or of twonucleic acid sequences, is determined using the algorithm of Karlin andAltschul (PNAS USA 87:2264-2268, 1990), modified as in Karlin andAltschul. PNAS USA 9.0:5873-5877, 1993). Such an algorithm isincorporated into the NBLAST and XBLAST programs of Altschul et al. (J.Mol. Biol. 215:403-410, 1990). BLAST nucleotide searches are performedwith the NBLAST program, score=100, wordlength=12. BLAST proteinsearches are performed with the XBLAST program, score=50, wordlength=3.To obtain gapped alignment for comparison purposes GappedBLAST isutilized as described in Altschul et al. (Nucleic Acids Res.25:3389-3402, 1997). When utilizing BLAST and GappedBLAST programs thedefault parameters of the respective programs (e.g., XBLAST and NBLAST)are used to obtain nucleotide sequences homologous to a nucleic acidmolecule of the invention.

The nucleotide sequence of the obtained cDNA is determined to find anopen reading frame, and thereby the amino acid sequence of the proteinof the invention can be obtained. The cDNA obtained may also be used asa probe for screening a genomic library to isolate a genomic DNA.

More specifically, mRNAs may first be prepared from a cell, tissue, ororgan in which the protein of the invention is expressed (e.g. tissuessuch as liver and kidney). Known methods can be used to isolate mRNAs;for instance, total RNA can be prepared by guanidine ultracentrifugation(Chirgwin et al., Biochemistry 18:5294-5299, 1979) or the AGPC method(Chomczynski et al., Anal. Biochem. 162:156-159, 1987). mRNA may then bepurified from total RNA using mRNA Purification Kit (Pharmacia) andsuch, alternatively, mRNA may be directly purified by QuickPrep mRNAPurification Kit (Pharmacia).

The obtained mRNA is used to synthesize cDNA using reversetranscriptase. cDNA may be synthesized by using a kit such as the AMVReverse Transcriptase First-strand cDNA Synthesis Kit (Seikagaku Kogyo).Alternatively, cDNA may be synthesized and amplified following the5′-RACE method (Frohman et al., Proc. Natl. Acad. Sci. U.S.A.85:8998-9002, 1988; Belyavsky et al., Nucleic Acids Res. 17:2919-2932,1989) which uses primers described herein, the 5′-Ampli FINDER RACE Kit(Clontech), and polymerase chain reaction (PCR).

A desired DNA fragment is prepared from the PCR products and ligatedwith a vector DNA. The recombinant vectors are used to transform E. Coliand such, and a desired recombinant vector is prepared from a selectedcolony. The nucleotide sequence of the desired DNA is verified byconventional methods, such as dideoxynucleotide chain termination.

A DNA of the invention may be designed to have a sequence that isexpressed more efficiently by taking into account the frequency of codonusage in the host to be used for expression (Grantham et al., NucleicAcids Res. 9:43-74, 1981). The DNA of the present invention may bealtered by a commercially available kit or a conventional method. Forinstance, the DNA may be altered by digestion with restriction enzymes,insertion of a synthetic oligonucleotide or an appropriate DNA fragment,addition of a linker, or insertion of the initiation codon (ATG) and/orthe stop codon (TAA, TGA, or TAG).

The DNA of the present invention also include a DNA hybridizing to a DNAconsisting of the nucleotide sequence of SEQ ID NO:1 and encoding aprotein functionally equivalent to the above-mentioned protein of thepresent invention. Those skilled in the art can properly select theappropriate hybridization conditions, and specifically theabove-mentioned conditions can be used. Under these conditions, thehigher the temperature, the higher the homology of the obtained DNA willbe. The above-mentioned hybridizing DNA is preferably a naturallyoccurring DNA, for example, cDNA or chromosomal DNA.

The present invention also provides a vector into which a DNA of thepresent invention is inserted. The vectors of the present invention areuseful for maintaining the DNA of the present invention within hostcells or expressing the protein of the invention.

When the E. coli is used as a host cell, there is no limitation otherthan that the vector should have an “ori” to amplify and mass-producethe vector in E. coli (e.g., JM109. DH5α, HB101, or XL1Blue), and amarker gene for selecting the transformed E. coli (e.g., adrug-resistance gene selected by a drug such as ampicillin,tetracycline, kanamycin, or chloramphenicol). For example, M13-seriesvectors, pUC-series vectors, pBR322, pBluescript, pCR-Script, and suchcan be used. pGEM-T, pDIRECT, pT7, and so on can also be used forsubcloning and excision of the cDNA as well as the vectors describedabove. When a vector is used to produce a protein of the presentinvention, an expression vector is especially useful. The expressionvector, for example, to be expressed in E. coli should have the abovecharacteristics to be amplified in E. coli. When E. coli, such as JM109,DH5α, HB101, or XL1 Blue, is used as the host cell, the vector shouldhave a promoter such as lacZ promoter (Ward et al., Nature 341:544-546,1989; FASEB J. 6:2422-2427, 1992), araB promoter (Better et al., Science240:1041-1043, 1988), or T7 promoter that can efficiently promote theexpression of the desired gene in E. coli. Other examples of the vectorsare pGEX-5×-1 (Pharmacia), “QIAexpress system” (Qiagen), pEGFP, and pET(for this vector, BL21, a strain expressing T7 RNA polymerase, ispreferably used as the host).

Further, the vector may contain a signal sequence for the secretion ofpolypeptides. The pelB signal sequence (Lei et al., J. Bacteriol.169:4379, 1987) can be used as a signal sequence for secretion ofproteins, when the proteins are intended to be produced in the periplasmof E. coli. Introduction of the vector into a host cell can beperformed, for example, by the calcium chloride method orelectroporation.

In addition to the vectors for E. coli, for example, the vector forproducing the proteins of this invention may be a mammal-derivedexpression vector (e.g., pcDNA3 (Invitrogen), pEGF-BOS (Nucleic AcidsRes. 18(17): 5322, 1990), pEF, and pCDM8), an insect cell-derivedexpression vector (e.g., “Bac-to-BAC baculovairus expression system”(GibcoBRL) and pBacPAK8), a plant-derived expression vector (e.g., pMH1and pMH2), an animal virus-derived expression vector (e.g., pHSV, pMV,and pAdexLcw), a retrovirus-derived expression vector (e.g., pZIPneo),an yeast-derived expression vector (e.g., “Pichia Expression Kit”(Invitrogen), pNV11, and SP-Q01), a Bacillus subtilis-derived expressionvector (e.g., pPL608 and pKTH50).

In order to express proteins in animal cells, such as CHO, COS, andNIH3T3 cells, the vector should have a promoter necessary for expressionin such cells, e.g., SV40 promoter (Mulligan et al., Nature 277:108,1979), MMLV-LTR promoter, EF1α promoter (Mizushima et al., Nucleic AcidsRes. 18:5322, 1990), CMV promoter, etc., and more preferably it has amarker gene for selecting transformants (for example, a drug resistancegene selected by a drug (e.g., neomycin. G418, etc.)). Examples ofvectors with these characteristics include pMAM, pDR2, pBK-RSV, pBK-CMV,pOPRSV, pOP13, and so on.

The method using CHO cells deficient in nucleic acid synthetic pathwaysas the host, and incorporating a vector (such as pCHOI) with a DHFR genethat compensates for the deficiency and amplifying the vector withmethotrexate (MTX) can be mentioned as an example method for stablyexpressing a gene and amplifying the copy number in cells. And as amethod for transient expression, a method transforming the COS cells,which have the gene for SV40 T antigen on the chromosome, with a vector(such as pcDNA3) having the SV40 replication origin can be mentioned.The origin used for replication may be those of polyomavirus,adenovirus, bovine papilloma virus (BPV), and the like. In addition, theexpression vector may include a selection marker gene for amplificationof the gene copies in host cells. Examples of such markers include, butare not limited to, the aminoglycoside transferase (APH) gene, thethymidine kinase (TK) gene, the E. coli xanthine-guanine phosphoribosyltransferase (Ecogpt) gene, and the dihydrofolate reductase (dhfr) gene.

The DNA of the present invention can be expressed in animals by, forexample, inserting a DNA of the invention into an appropriate vector andintroducing the vector into a living body by the retrovirus method,liposome method, cationic liposome method, adenovirus method, and so on.Thus, gene therapy can be conducted for diseases caused by mutations inthe “C-NT2RP3001495” gene of this invention. The vectors used include,but are not limited to, adenoviral vectors (e.g., pAdexlcw) andretroviral vectors (e.g., pZIPneo). General techniques for genemanipulation, such as insertion of the DNA of the invention into avector, can be performed according to conventional methods (MolecularCloning, 5.61-5.63). The DNA of this invention can be administered tothe living body by an ex vivo method or in vivo method.

The present invention also provides a host cell into which the vector ofthe present invention has been introduced. The host cell into which thevector of the invention is introduced is not particularly limited. E.coli and various animal cells can be used. The host cell of thisinvention can be used as, for example, a production system for producingor expressing the protein of the invention. The production system forproducing a protein of the invention may be both in vitro or in vivoproduction system. For in vitro production, eukaryotic cells orprokaryotic cells can be used.

Useful eukaryotic host cells may be animal, plant, or fungi cells. Asanimal cells, mammalian cells such as CHO (J. Exp. Med. 108:945, 1995),COS, 3T3, myeloma, baby hamster kidney (BHK), HeLa, or Vero cells,amphibian cells such as Xenopus oocytes (Valle et al. Nature291:340-358, 1981), or insect cells such as Sf9, Sf21, or Tn5 cells canbe used. CHO cells lacking DHFR gene (dhfr-CHO) (Proc. Natl. Acad. Sci.U.S.A. 77:4216-4220, 1980) or CHO K-1 (Proc. Natl. Acad. Sci. U.S.A.60:1275, 1968) may also be used. Among the animal cells, CHO cells areparticularly preferable for high-level expression. The vector can beintroduced into the host cell by, for example, the calcium phosphatemethod, the DEAE-dextran method, cationic liposome DOTAP (BoehringerMannheim) method, electroporation, lipofection, etc.

As plant cells, for example, plant cells originating from Nicotianatabacum are known as protein production system and may be used as calluscultures. As fungi cells, yeast cells such as Saccharomyces, includingSaccharomyces cerevisiae, or filamentous fungi such as Aspergillus,including Aspergillus niger, are known.

Useful prokaryotic cells include bacterial cells, such as E. coli, forexample, JM109, DH5a, and HB101, or Bacillus subtilis.

These cells are transformed by a desired DNA, and the resultingtransformants are cultured in vitro to obtain the protein. Transformantscan be cultured using known methods. Culture medium such as DMEM, MEM,RPM11640, or IMDM may be used for animal cells. The culture medium canbe used with or without serum supplement such as fetal calf serum (FCS).The pH of the culture medium is preferably between about 6 and 8. Cellsare typically cultured at about 30 to 40° C. for about 15 to 200 hr, andthe culture medium may be replaced, aerated, or stirred if necessary.

Animal and plant hosts may be used for in vivo production. For example,a desired DNA can be introduced into an animal or plant host. Encodedproteins are produced in vivo, and then are recovered. These animal andplant hosts are included in host cells of the present invention.

Animals to be used for the production system described above includemammals and insects. Mammals such as goat, porcine, sheep, mouse, andbovine may be used (Vicki Glaser, SPECTRUM Biotechnology Applications(1993)). Alternatively, the mammals may be transgenic animals.

For instance, a desired DNA may be prepared as a fusion gene, fused witha gene such as goat β casein gene which encodes a protein specificallyproduced into milk. DNA fragments comprising the fusion gene areinjected into goat embryos, which are then transplanted back to femalegoats. Proteins of interest can be recovered from milk produced by thetransgenic goats (i.e., those born from the goats that had received theembryos) or from their offspring. To increase the amount of milkcontaining the proteins produced by transgenic goats, hormones may beappropriately administered to them (Ebert et al., Bio/Technology12:699-702, 1994).

Alternatively, insects, such as the silkworm, may be used. Baculovirusesinto which the DNA encoding the protein of interest is inserted can beused to infect silkworms, and the desired protein can be recovered fromtheir body fluid (Susumu et al., Nature 315:592-594, 1985).

As plants, for example, tobacco can be used. In use of tobacco, DNAencoding the protein of interest may be inserted into a plant expressionvector, such as pMON530, which is introduced into bacteria, such asAgrobacterium tumefaciens. Then the bacteria is used to infect tobacco,such as Nicotiana tabacum, and a desired polypeptide can be recoveredfrom their leaves (Julian et al., Eur. J. Immunol. 24:131-138, 1994).

A protein of the present invention obtained as above may be isolatedfrom inside or outside of the host cells (e.g., culture media), andpurified as a substantially pure homogeneous protein. The method forprotein isolation and purification is not limited to any specificmethod; in fact, any standard method may be used. For instance, columnchromatography, filter, ultrafiltration, salt precipitation, solventprecipitation, solvent extraction, distillation, immunoprecipitation,SDS-polyacrylamide gel electrophoresis, isoelectric pointelectrophoresis, dialysis, recrystallization, and so on may beappropriately selected and combined to isolate and purify the protein.

For example, affinity chromatography, ion-exchange chromatography,hydrophobic chromatography, gel filtration, reverse phasechromatography, adsorption chromatography, and such may be used forchromatography (Daniel R. Marshak et al., Strategies for ProteinPurification and Characterization: A Laboratory Course Manual. Ed., ColdSpring Harbor Laboratory Press, 1996). These chromatographies may beperformed by liquid chromatography such as HPLC and FPLC. Thus, thepresent invention includes highly purified proteins, purified by theabove methods.

A protein of the present invention may be optionally modified orpartially deleted by treating it with an appropriate proteinmodification enzyme before or after purification. Useful proteinmodification enzymes include, but are not limited to, trypsin,chymotrypsin, lysylendopeptidase, protein kinase, glucosidase, and soon.

The present invention also provides antibodies that bind to the proteinof the invention. The antibody of the invention may take any form,including monoclonal antibody, as well as polyclonal antibodies.Furthermore, antiserum obtained by immunizing an animal such as rabbitwith the protein of the invention, all classes of polyclonal andmonoclonal antibodies, human antibodies, and humanized antibodiesproduced by genetic recombination are included.

A protein of the invention used as the antigen to obtain antibodies maybe derived from any animal species, but preferably it is derived from amammal, such as a human, mouse, or rat, and more preferably from human.A human-derived protein may be obtained from the nucleotide or aminoacid sequences disclosed herein.

Herein, a protein used as an antigen may be a complete protein orpartial peptides thereof. A partial peptide may be, for example, anamino (N)-terminal or carboxy (C)-terminal fragment of the protein.Herein, an antibody is defined as an antibody that reacts with eitherthe full-length or a fragment of the protein.

A gene encoding a protein of the invention or its fragment may beinserted into a known expression vector, which is used to transform ahost cell as described herein. The desired protein or its fragment maybe recovered from the outside or inside of the host cell by any standardmethod, and may be used as an antigen. Alternatively, cells expressingthe protein or their lysates, or a chemically synthesized protein may beused as an antigen. Short peptides are preferably used as antigens byappropriately combining them with carrier proteins such as keyholelimpet hemocyanin, bovine serum albumin, and ovalbumin.

Any mammalian animal may be immunized with the antigen, but preferablythe compatibility with parental cells used for cell fusion is taken intoaccount. In general, animals of Rodentia, Lagomorpha, or Primates areused.

Animals of Rodentia include, for example, mouse, rat, and hamster.Animals of Lagomorpha include, for example, rabbit. Animals of Primatesinclude, for example, a monkey of Catarrhini (old world monkey) such ascrab-eating monkey, rhesus monkey, sacred baboon, or chimpanzee.

Methods for immunizing animals with antigens are known in the art. Forinstance, intraperitoneal injection or subcutaneous injection ofantigens is used as a standard method for immunization of mammals. Morespecifically, antigens may be diluted and suspended in an appropriateamount with phosphate buffered saline (PBS), physiological saline, etc.If desired, the antigen suspension may be mixed with an appropriateamount of a standard adjuvant, such as Freund's complete adjuvant, madeinto emulsion, and then administered to mammals. Preferably, it isfollowed by several administrations of antigen mixed with anappropriately amount of Freund's incomplete adjuvant every 4 to 21 days.An appropriate carrier may also be used for immunization. Afterimmunization as above, serum is examined for increase of the amount ofdesired antibodies by a standard method.

Polyclonal antibodies against the proteins of the present invention maybe prepared by collecting blood from the immunized mammal examined forthe increase of desired antibodies in the serum, and by separating serumfrom the blood by any conventional method. Serum containing thepolyclonal antibodies, or if necessary, a fraction containing thepolyclonal antibodies may be isolated from the serum to be used as thepolyclonal antibodies of the present invention. For example,immunoglobulin G or M can be prepared by using an affinity columncoupled with the protein of the invention to obtain the fractionexclusively recognizing the protein of the invention, and then,purifying the fraction by using protein A or protein G column.

To prepare monoclonal antibodies, immune cells are collected from themammal immunized with the antigen and checked for the increased level ofdesired antibodies in the serum as described above, and are subjected tocell fusion. The immune cells used for cell fusion are preferablyobtained from spleen. The other parent cell which is fused with theabove immune cell is preferably a mammalian myeloma cell, and morepreferably a myeloma cell that has acquired a special feature that canbe used for selection of fusion cells by drugs.

Cell fusion of the above immune cell and myeloma cell may be performedby any standard method, such as those described in the literature(Galfre et al., Methods Enzymol. 73:3-46, 1981).

Hybridomas obtained by the cell fusion may be selected by cultivatingthem in a standard selection medium, such as HAT medium (hypoxanthine,aminopterin, and thymidine containing medium). The cell culture istypically continued in the HAT medium for several days to several weeks,the time being sufficient to allow all the other cells, except desiredhybridoma (non-fused cells), to die. Then, the standard limitingdilution is performed to screen and clone a hybridoma cell producing thedesired antibody.

Besides the above method, in which a nonhuman animal is immunized withan antigen for preparing hybridoma, human lymphocytes such as thatinfected by EB virus may be immunized with a protein, protein expressingcells, or their lysates in vitro. Then, the immunized lymphocytes arefused with human-derived myeloma cells that is capable of indefinitelydividing, such as U266, to yield a hybridoma producing a desired humanantibody, able to bind to the protein can be obtained (UnexaminedPublished Japanese Patent Application (JP-A) No. Sho 63-17688).

Subsequently, the hybridomas thus obtained are transplanted into theabdominal cavity of a mouse from which the ascites is collected. Themonoclonal antibodies thus obtained can be purified by, for example,ammonium sulfate precipitation or by column chromatography using aprotein A or protein G column, a DEAE ion exchange column, an affinitycolumn to which the protein of the invention is coupled, and such. Theantibody of the invention can be used not only for purifying anddetecting the protein of the invention, but also as a candidate for anagonist or antagonist to the protein of the present invention. It isalso expected to use the antibody for antibody therapy of diseasesassociated with the protein of this invention. When the antibodyobtained is administered to the human body (antibody therapy), humanantibodies or humanized antibodies are preferred to reduceimmunogenicity.

For example, transgenic animals having a repertory of human antibodygenes may be immunized with a protein, protein expressing cells, ortheir lysates as an antigen. Antibody producing cells are collected fromthe animals, and fused with myeloma cells to obtain hybridoma, fromwhich human antibodies against the protein can be prepared (seeWO92-03918, WO93-2227, WO94-02602, WO94-25585, WO96-33735, andWO96-34096).

Alternatively, an immune cell, such as an immunized lymphocyte,producing antibodies may be immortalized by an oncogene and used forpreparing monoclonal antibodies.

Monoclonal antibodies thus obtained can also be recombinantly preparedusing genetic engineering techniques (see, for example, Borrebaeck C. A.K. and Larrick J. W. Therapeutic Monoclonal Antibodies, published in theUnited Kingdom by MacMillan Publishers LTD (1990)). A DNA encoding anantibody may be cloned from an immune cell, such as hybridomas orimmunized lymphocytes producing the antibody; inserted into anappropriate vector; and introduced into host cells to prepare arecombinant antibody. The present invention also includes recombinantantibodies prepared as described above.

The antibody of the present invention may be a fragment of an antibodyor modified antibody, so long as it binds to the protein of theinvention. For instance, the antibody fragment may be Fab, F(ab′)₂, Fv,or single chain Fv (scFv), in which Fv fragments from H and L chains areligated by an appropriate linker (Huston et al., Proc. Natl. Acad. Sci.U.S.A. 85:5879-5883, 1988). More specifically, an antibody fragment maybe generated by treating an antibody with an enzyme such as papain orpepsin. Alternatively, a gene encoding the antibody fragment may beconstructed; inserted into an expression vector; and expressed in anappropriate host cell (see, for example, Co et al., J. Immunol.152:2968-2976, 1994; Better et al., Methods Enzymol. 178:476-496, 1989;Pluckthun et al., Methods Enzymol. 178:497-515, 1989; Lamoyi, MethodsEnzymol. 121:652-663, 1986; Rousseaux et al., Methods Enzymol.121:663-669, 1986; Bird et al., Trends Biotechnol. 9:132-137, 1991).

An antibody may be modified by conjugation with a variety of molecules,such as polyethylene glycol (PEG). The antibody of the present inventionincludes such modified antibodies. A modified antibody can be obtainedby chemically modifying an antibody. These modification methods havebeen already established in the field.

Alternatively, the antibody of the present invention may be obtained asa chimeric antibody, between a variable region derived from nonhumanantibody and the constant region derived from human antibody, or as ahumanized antibody, comprising the complementarity determining region(CDR) derived from nonhuman antibody, the frame work region (FR) derivedfrom human antibody, and the constant region. Such antibodies can beprepared by using known technology.

Obtained antibodies may be purified to homogeneity. The antibodies canbe separated and purified by using standard methods for proteinseparation and purification. For instance, column chromatography such asaffinity chromatography, filter, ultrafiltration, salt precipitation,dialysis, SDS-polyacrylamide gel electrophoresis, isoelectric pointelectrophoresis, and so on may be appropriately selected and combined toisolate and purify the antibody (Antibodies: A Laboratory Manual. EdHarlow and David Lane, Cold Spring Harbor Laboratory, 1988), but methodsare not limited to them. The concentration of the antibody obtained asdescribed above can be determined by the measurement of absorbance,enzyme-linked immunosorbent assay (ELISA), or others.

Columns for affinity chromatography include protein A column and proteinG column. For example, protein A column includes Hyper D, POROS,Sepharose F. F. (Pharmacia) and the like.

In addition to affinity chromatography, chromatographic methods include,for example, ion exchange chromatography, hydrophobic chromatography,gel filtration, reverse-phase chromatography, adsorption chromatographyand others (“Strategies for Protein Purification and Characterization: ALaboratory Course Manual” Ed Daniel R. Marshak et al., Cold SpringHarbor Laboratory Press, 1996). These chromatographic methods can beconducted by using liquid chromatography such as HPLC and FPLC.

For example, absorbance measurement, enzyme-linked immunosorbent assay(ELISA), enzyme immunoassay (EIA), radioimmunoassay (RIA), orimmunofluorescence may be used to measure the antigen binding activityof the antibody of the invention. In ELISA, the antibody of the presentinvention is immobilized on a plate; the protein of the invention isapplied to the plate; and then a sample containing a desired antibody,such as culture supernatant of antibody producing cells or purifiedantibodies, is applied. Then, a secondary antibody that recognizes theprimary antibody and which is labeled with an enzyme such as alkalinephosphatase is applied, and the plate is incubated. After washing, anenzyme substrate, such asp-nitrophenyl phosphate, is added to the plate,and the absorbance is measured to evaluate the antigen binding activityof the sample. A fragment of the protein, such as a C-terminal fragment,may be used as a protein. BIAcore (Pharmacia) may be used to evaluatethe activity of the antibody according to the present invention.

The above methods allow for the detection or measurement of the proteinof the invention, by exposing the antibody of the invention to a sampleassumed to contain the protein of the invention, and detecting ormeasuring the immune complex formed by the antibody and the protein.Because the method of detection or measurement of the protein accordingto the invention can specifically detect or measure a protein, themethod may be useful in a variety of experiments in which the protein isused.

The present invention also provides a polynucleotide containing at least15 nucleotides complementary to the DNA (SEQ ID NO:1) encoding the humanprotein “C-NT2RP3001495” or the complementary strand thereof.

Herein, the term “complementary strand” is defined as one strand of adouble strand DNA composed of A:T and G:C base pair to the other strand.Also, “complementary” is defined as not only those completely matchingwithin a continuous region of at least 15 nucleotides, but also having ahomology of at least 70%, favorably 80% or higher, more favorably 90% orhigher, and most favorably 95% or higher within that region. Thehomology may be determined using the algorithm described herein.

Such a nucleic acid includes probes and primers used for the detectionand amplification of DNA encoding the inventive protein; probes andprimers used for the detection of expression of the DNA; and nucleotideand nucleotide derivatives (e.g., antisense oligonucleotide andribozyme, or DNAs encoding them, etc.) used for the regulation ofexpression of the inventive protein. In addition, such a nucleic acidcan also be used for the preparation of DNA chip.

When used as primers, such nucleic acids are complementary at the 3′end, and restriction enzyme recognition sequences or tags can be addedto the 5′ end.

The antisense oligonucleotides include, for example, antisenseoligonucleotides hybridizing to any region of the nucleotide sequence ofSEQ ID NO:1. The antisense oligonucleotide is preferably an antisense ofa continuous sequence of a length of 15 nucleotides or longer within thenucleotide sequence of SEQ ID NO:1. More preferably, the abovecontinuous sequence of a length of 15 nucleotides or longer contains thetranslation initiation codon.

A derivative or modified form of antisense oligonucleotide may also beused. The modified antisense oligonucleotides may be those modified withlower alkylphosphonate such as methylphosphonate and ethylphosphonate;phosphorothioate; phosphoroamidate; and so on.

Herein, an antisense oligonucleotide is not restricted to those in whichall nucleotides are complementary to the corresponding nucleotideswithin a given region of a DNA or mRNA; so long as it can specificallyhybridize with the nucleotide sequences of SEQ ID NO:1, it may have oneor more nucleotide mismatches.

A derivative of the antisense oligonucleotide of the present inventionmay act on cells producing the protein of the invention and may bind toa DNA or mRNA encoding the protein, whereby inhibiting the expression ofthe protein of the invention by inhibiting its transcription ortranslation, or by promoting the degradation of mRNA, and therebyinhibiting the function of the protein of the invention.

A derivative of the antisense oligonucleotide of the present inventionmay be mixed with appropriate carriers which are inactive against thederivative, and may be used as a medicine for externally applicationsuch as salve or poultice.

If necessary, it may be mixed with an excipient, isotonizing agent,solubilizing agent, stabilizer, preservative, pain-killer, or the like,and prepared as a tablet, powder, granule, capsule, liposome capsule,injectable solution, liquid formulation, nose drops, freeze-dried agent,etc. The above may be achieved according to standard methods.

For treating patients, a derivative of an antisense oligonucleotide ofthe present invention may be, for example, directly applied to theaffected area of a patient, or administered into blood vessels so as tofinally reach the affected area. Moreover, the derivative may beencapsulated in antisense-encapsulating materials such as liposome,poly-L-lysine, lipid, cholesterol, lipofectin, or their derivative inorder to increase durability and/or membrane permeability.

Dose of the derivative of the antisense oligonucleotide of the presentinvention may be appropriately adjusted depending on the patient'sconditions, and a favorable amount such as 0.1 to 100 mg/kg, or morepreferably 0.1 to 50 mg/kg may be administered.

As the antisense oligonucleotides of the present invention inhibitexpression of the protein of the invention, they find utility asinhibitors of the biological activity of the protein of the invention.An inhibitor of expression comprising the antisense oligonucleotide ofthe present invention is useful because it can inhibit the biologicalactivity of the protein of the invention.

The protein of the invention may be used to screen for compounds thatbind to the protein of the present invention. Specifically, the proteinmay be used in methods of screening for compounds, which methodcomprises the steps of exposing the protein of the present invention toa test sample in which a compound binding to the protein is expected tobe contained; and selecting the compound having the activity of bindingto the protein.

The proteins of the invention used for screening may be recombinant ornatural proteins, or partial peptides. Alternatively, they may beexpressed on the surface of cells or in the form of a membrane fraction.There is no particular restriction on the test sample as it includes,for example, cell extract, cell culture supernatant, product offermentation microorganism, extract from marine organism, extract fromplant, purified or crude protein, peptide, non-peptide compound,synthetic low-molecular-weight compound, natural compound, etc. Theinventive protein to be contacted with a test sample can be contactedwith the test sample, for example, as a purified protein, as a solubleprotein, in a form of protein immobilized on carriers, as a fusionprotein with other proteins, in a form of protein presented on cellmembrane, as a membrane fraction.

Many methods known to those skilled in the art can be used to screenproteins capable of binding to the inventive protein. Such screening canbe carried out, for example, by the immunoprecipitation method.Specifically, the method can be carried out as follows. The geneencoding a protein of this invention is expressed by inserting the geneinto a vector for foreign gene expression in pSV2neo, pcDNA I, pCD8, andsuch, and expressing the gene in animal cells, etc. Any generally usedpromoters may be employed for the expression, including the SV40 earlypromoter (Rigby In Williamson (ed.), Genetic Engineering, Vol. 3.Academic Press, London, p. 83-141 (1982)), EF-1α promoter (Kim et al.,Gene 91:217-223, 1990), CAG promoter (Niwa et al., Gene 108:193-200,1991), RSV LTR promoter (Cullen, Methods in Enzymology 152:684-704,1987), SR α promoter (Takebe et al., Mol. Cell. Biol. 8:466, 1988), CMVimmediate early promoter (Seed et al., Proc. Natl. Acad. Sci. U.S.A.84:3365-3369, 1987), SV40 late promoter (Gheysen et al., J. Mol. Appl.Genet. 1:385-394, 1982), Adenovirus late promoter (Kaufman et al., Mol.Cell. Biol. 9:946, 1989), HSV TK promoter, etc.

Transfer of a foreign gene into animal cells for its expression can beperformed by any of the following methods, including the electroporationmethod (Chu et al., Nucl. Acid Res. 15:1311-1326, 1987), the calciumphosphate method (Chen et al., Mol. Cell. Biol. 7:2745-2752, 1987), theDEAE dextran method (Lopata et al., Nucl. Acids Res. 12:5707-5717, 1984;Sussman et al., Mol. Cell. Biol. 4:1642-1643, 1985), the lipofectinmethod (Derijard, Cell. 7:1025-1037, 1994; Lamb et al., Nature Genetics5:22-30, 1993; Rabindran et al., Science 259:230-234, 1993), etc.

The protein of this invention can be expressed as a fusion proteinhaving a recognition site for a monoclonal antibody by introducing therecognition site (epitope) for the monoclonal antibody, the specificityof which has been established, into the N- or C-terminus of the proteinof this invention. For this purpose, commercial epitope-antibody systemscan be utilized (Igaku, Experimental Medicine 13:85-90, 1995). Vectorswhich can express fusion proteins with the β-galactosidase,maltose-binding protein, glutathione S-transferase, green fluorescenceprotein (GFP), and such, via the multi-cloning site are commerciallyavailable.

There is also a report that a fusion protein may be prepared byintroducing only small epitope portions consisting of several to a dozenamino acid residues so as not to change the property of the protein ofthe present invention by the fusion. For example, epitopes such aspolyhistidine (His-tag), influenza hemagglutinin (HA), human c-myc,FLAG, Vesicular stomatitis virus glycoprotein (VSV-GP), T7 gene 10protein (T7-tag), human herpes simplex virus glycoprotein (HSV-tag),E-tag (epitope on the monoclonal phage), and such, and monoclonalantibodies to recognize them can be utilized as the epitope-antibodysystem for screening proteins binding to the protein of this invention(Igaku, Experimental Medicine 13:85-90, 1995).

In immunoprecipitation, immune complexes are formed by adding theseantibodies to the cell lysate prepared using suitable surfactants. Theimmune complex comprises a protein of this invention, a proteincomprising the binding ability with the protein, and an antibody.Immunoprecipitation can be also performed by using antibodies against aprotein of this invention, besides using antibodies against theabove-described epitopes. An antibody to a protein of this invention canbe prepared, for example, by inserting a gene encoding the protein ofthe invention into an appropriate expression vector of E. coli toexpress it in the bacterium, purifying the expressed protein, andimmunizing rabbits, mice, rats, goats, chicken, and such against thepurified protein. The antibody can be also prepared by immunizing theabove-described animals against synthetic partial peptides of theprotein of the present invention.

Immune complexes can be precipitated using, for example, Protein ASepharose and Protein G Sepharose when the antibody is a murine IgGantibody. In addition, if a protein of this invention is prepared as afusion protein with the epitope, such as GST, an immune complex can beformed by using a substance specifically binding to these epitopes, suchas glutathione-Sepharose 4B, in the same mannere as in the use of theantibody against the protein of the present invention.

Immune precipitation, in general, may be carried out according to, orfollowing the method described in the literature (Harlow, E. and Lane,D.: Antibodies, pp. 511-552, Cold Spring Harbor Laboratory publications,New York (1988)).

SDS-PAGE is generally used for the analysis of immunoprecipitatedproteins. Bound proteins can be analyzed based on the molecular weightsof proteins using a gel of an appropriate concentration. In this case,although proteins bound to a protein of this invention, in general, arehardly detectable by the usual protein staining method, such asCoomassie staining and silver staining, the detection sensitivity can beimproved by culturing cells in a medium containing radioisotopes, suchas ³⁵S-methionine and ³⁵S-cysteine, to label proteins inside the cells,and detecting the labeled proteins. Once the molecular weight of theprotein is determined, the desired protein can be purified directly fromthe SDS-polyacrylamide gel and can be sequenced.

In addition, proteins binding to a protein of this invention can beisolated using the West-western blotting method (Skolnik et al., Cell65:83-90, 1991) with the protein of this invention. Namely, cDNA isisolated from cells, tissues, and organs, in which the protein bindingto a protein of this invention is expected to be expressed (e.g. liverand kidney), and transferred into a phage vector (for example, λgt11,ZAP, and such) to prepare a cDNA library, which is then expressed onLB-agarose plates. The protein thus expressed is fixed on a filter;reacted with the labeled, purified protein of this invention; andplaques expressing a protein bound to a protein of this invention can bedetected by the label. Methods for labeling the proteins of thisinvention include methods using the binding activity of biotin andavidin; methods using antibodies specifically binding to the proteins ofthis invention, or peptides or polypeptides fused with the protein ofthis invention (e.g., GST); methods using the radioisotopes; methodsusing fluorescence; etc.

Alternatively, in another embodiment of the method for screening of thepresent invention, the two-hybrid system utilizing cells may be used(Fields et al., Trends Genet. 10:286-292, 1994; Dalton et al., Cell68:597-612, 1992; “MATCHMAKER Two-Hybrid System”, “Mammalian MATCHMAKERTwo-Hybrid Assay Kit”, “MATCHMAKER One-Hybrid System (all fromClontech), “HybriZAP Two-Hybrid Vector System” (Stratagene)). In thetwo-hybrid system, an inventive protein or a partial peptide thereof isfused with the SRF DNA-binding region or GAL4 DNA-binding region, andthen is expressed in yeast cells; a cDNA library, which express proteinsin the form of fusion protein with the VP16 or GAL4 transcriptionactivation region, is prepared from cells that are predicted to expressa protein binding to an inventive protein; the resulting cDNA library isintroduced into the above-mentioned yeast cells; and then a cDNA derivedfrom the library is isolated from a detected positive clone (when aprotein binding to the inventive protein is expressed in yeast cells,the reporter gene is activated by the binding of the two proteins, andthus positive clones are detectable). A protein encoded by the cDNA canbe prepared after the isolated cDNA is introduced and expressed in E.coli. Thus it is possible to prepare a protein binding to an inventiveprotein or the encoding gene. Reporter genes to be used in thetwo-hybrid system include, but are not limited to, for example, Ade2gene, LacZ gene, CAT gene, luciferase gene, PAI-1 (Plasminogen activatorinhibitor type1) gene in addition to HIS3 gene. The screening by thetwo-hybrid method can be conduced by using mammalian cells or others inaddition to yeast.

Compounds binding to a protein of the present invention can be screenedby affinity chromatography. For example, a protein of the invention isimmobilized on a carrier of an affinity column, and a test sample, inwhich a protein binding to the protein of the invention is supposed tobe expressed, is applied to the column. A test sample herein may be, forexample, cell extracts, cell lysates, etc. After loading the testsample, the column is washed, and proteins bound to a protein of theinvention can be prepared.

The amino acid sequence of the resulting protein is then analyzed. Basedon the result, an oligo-DNA is synthesized and used as the probe toscreen a cDNA library. This can provide a DNA encoding the protein.

In the present invention, a biosensor on the basis of surface plasmonresonance phenomenon can be used as a means to detect or assay the boundcompounds. By utilizing the biosensor on the basis of surface plasmonresonance phenomenon, the interaction between the inventive protein anda test compound can be observed as a surface plasmon resonance signal inreal time using a small amount of protein without labeling (e.g.,BIAcore, Pharmacia). Thus the binding between the inventive protein andthe test compound can be assessed by using biosensor of BIAcore, or thelike.

In addition, methods are known in the art for isolating compoundsbinding to a protein of the invention, which are not limited only toproteins (including agonists and antagonists). Such methods include, forexample, the method of screening for a molecule binding to a protein ofthe invention by contacting a synthetic compound or natural substancebank, or a random phage peptide display library with an immobilizedprotein of the invention, and the high-throughput screening method usinga combinatorial chemistry technique (Wrighton et al., Science273:458-64, 1996; Verdine G. L., Nature 384:11-13, 1996; Hogan J. C.Jr., Nature 384:17-9, 1996).

Compounds isolated by the screening of this invention are candidates foragents to regulate the activity of a protein of this invention, andthought to be applied to treatments for disorders caused by expressionaland functional abnormalities, and such of the protein, and diseaseswhich can be treated by controlling the activity of the protein.Compounds which can be obtained by the screening method of thisinvention, the partial structure of which is modified by addition,deletion and/or substitution, are also included in the compounds bindingto the protein of this invention.

When a protein of this invention or compounds isolated by the screeningof this invention are used as drugs for humans and other animals, forexample, mice, rats, guinea pigs, rabbits, chickens, cats, dogs, sheep,pigs, cattle, monkeys, baboons, and chimpanzees, they can beadministered by directly administering the protein or isolated compounditself to a patient or by administering it after formulated according toknown pharmaceutical methods. They can be administered, as the occasiondemands, for example, orally, as sugar-coated tablets, capsules, elixirsand microcapsules, or parenterally, in the form of sterile solutions inwater or other pharmaceutically acceptable liquids, or suspensions forinjections. For example, they may be formulated by appropriately mixingwith pharmaceutically acceptable carriers or media, specifically sterilewater, physiological saline, plant oil, emulsifying agents, suspendingagents, surfactants, stabilizers, seasonings, excipients, vehicles,anticeptics, binders, and such, in the unit dosage form required in agenerally accepted pharmaceutical procedure. Amounts of effectiveingredients in these pharmaceutical preparations are adjusted so as toobtain the appropriate dose in the specified range.

Additives which can be mixed in tablets and capsules include, forexample, binders such as gelatin, corn starch, tragacanth gum and arabicgum; excipients such as crystalline cellulose; bulking agents such ascorn starch, gelatin and alginic acid; lubricants such as magnesiumstearate; sweetening agents such as sucrose, lactose or saccharine; andflavors such as peppermint, Gaultheria adenothrix oil or cherry. Whenthe dispensing unit form is a capsule, liquid carriers, such as oil, canbe further added to the above-described materials; Sterile compositionsfor injection can be prescribed using vehicles such as distilled waterfor injection according to standard pharmaceutical procedure.

Aqueous solutions for injections include, for example, physiologicalsaline, and isotonic solutions containing: glucose and other supplementssuch as D-sorbitol, D-mannose, D-mannitol, sodium chloride, and such;and suitable solubilizers, for example, alcohols, more specifically,ethanol, polyalcohols such as propylene glycol, polyethylene glycol,non-ionic surfactants such as polysorbate 80 (™) and HCO-50 may be usedtogether.

Oily solutions, including sesame oil and soybean oil, and benzylbenzoate and benzyl alcohol may be used together as the solubilizer.Injections may be combined with buffers such as phosphate buffer andsodium acetate buffer; soothing agents such as procaine hydrochloride;stabilizers such as benzyl alcohol, phenols and antioxidants. Injectionsthus prepared are typically filled in suitable ampules.

The administration to patients is done by methods commonly known tothose skilled in the art, such as intraarterial, intravenous, orsubcutaneous injections, as well as intranasal, bronchial,intramuscular, percutaneous, or oral administrations. One skilled in theart can suitably select the dosage according to the body-weight or ageof a patient, or the method of administration. If the compound can beencoded by DNA, the DNA may be used for gene therapy by incorporatingthe DNA into a vector for gene therapy. Dosages and administrationmethods vary depending on the body-weight, age, symptoms, and such ofpatients, but those skilled in the art can appropriately select them.

Although the specific dosage of the protein of the invention changesaccording to the subject to be treated, the target organs, symptoms, andadministration methods, it is generally considered to be, for example,about 100 μg to 20 mg one day for an adult (as body-weight 60 kg) in theform of injections.

Though they vary depending on the symptoms, doses of compounds bindingto a protein of this invention or compounds regulating the activity ofsuch a protein may be generally in the range of about 0.1 to 100 mg,preferably about 1.0 to 50 mg, and more preferably about 1.0 to 20 mgper day for adults (based on the body weight 60 kg) in the case of oraladministration.

Though it varies depending on the subject to be administered, targetorgan, symptom and method of administration, a single dose of thecompounds for the parenteral administration is thought to be preferablyadministered, for example, when it is in the form of injection,intravenously to normal adults (based on the body weight 60 kg) in therange of about 0.01 to 30 mg, preferably about 0.1 to 20 mg, and morepreferably about 0.1 to 10 mg or thereabout per day. Doses converted onthe 60 kg body weight basis or the body surface area can be similarlyadministered to other animals.

All publications and patents cited herein are incorporated by referencein their entirety.

DESCRIPTION OF DRAWINGS

FIG. 1 is a schematic diagram showing the structural features of theamino acid sequences of human “C-NT2RP3001495” of the invention, chicken“12F08” and “HHCMA56”. The protein “C-NT2RP3001495” of the presentinvention contains WW domains and Adh short motif in the N-terminalregion.

DETAILED DESCRIPTION

The invention is illustrated more specifically with reference to thefollowing examples, but is not to be construed as being limited thereto.

EXAMPLE 1 Construction of a cDNA Library by the Oligo-Capping Method

The NT-2 neuron progenitor cells (Stratagene), teratocarcinoma cellsfrom human fetal testis, which can be differentiated into neurons by thetreatment with retinoic acid were cultured for two weeks after inductiontreatment by the addition of retinoic acid according to themanufacturer's instructions.

After the culture, the cells were collected, and mRNA was extractedaccording to the method described in the literature (Sambrook et al.,Molecular Cloning Second edition, Cold Spring harbor Laboratory Press1989). Then, poly(A)⁺ RNA was purified by using oligo dT cellulose.

This poly(A)⁺ RNA was used to construct a cDNA library by theoligo-capping method (Maruyama et al., Gene, 138:171-174, 1994). Usingthe Oligo-cap linker (agcaucgagu cggccuuguu ggccuacugg/SEQ ID NO:5) andthe Oligo-dT primer (gcggctgaag acggcctatg tggccttttt tttttttttt tt/SEQID NO:6), bacterial alkaline phosphatase (BAP) treatment, tobacco acidphosphatase (TAP) treatment, RNA ligation, the first strand cDNAsynthesis, and removal of RNA were performed according to the references(Suzuki et al., Protein, Nucleic acid and Enzyme 41:197-201, 1996;Suzuki et al., Gene 200:149-156, 1997). Then, 5′- and 3′-PCR primers(agcatcgagt cggccttgtt g/SEQ ID NO:7, and gcggctgaag acggcctatg t/SEQ IDNO:8, respectively) were used for performing PCR to convert the cDNAinto double stranded cDNA, which was then digested with SfiI. Then, theDraIII-cleaved pME18SFL3 (GenBank AB009864, expression vector) was usedfor cloning the cDNA in a unidirectional manner, and cDNA libraries wereobtained. The nucleotide sequence of the 5′- and 3′-ends of the cDNAclones was analyzed with a DNA sequencer (ABI PRISM 377, PE Biosystems)after sequencing reactions performed with the DNA sequencing reagents(Dye Terminator Cycle Sequencing FS Ready Reaction Kit, dRhodamineTerminator Cycle Sequencing FS Ready Reaction Kit, or BigDye TerminatorCycle Sequencing FS Ready Reaction Kit, PE Biosystems), according to theinstructions.

pME18SFL3 vector contains the SRα promoter and SV40 small t intron inthe upstream, as well as the SV40 polyA addition signal sequencedownstream of the cloning site, respectively. As the cloning site ofpME18SFL3 has asymmetrical DraIII sites, and the ends of cDNA fragmentscontain SfiI sites complementary to the DraIII sites, the cloned cDNAfragments can be unidirectionally inserted downstream of the SRαpromoter. Therefore, clones containing full-length cDNA can be expressedtransiently by introducing the obtained plasmid directly into COS cells.Thus, the clones can be analyzed very easily in terms of the proteinsthat are the gene products of the clones, or in terms of the biologicalactivities of the proteins.

EXAMPLE 2 Estimation of the Completeness at the 5′-Ends of the ClonesContained in the cDNA Libraries Constructed by the Oligo-Capping Method

The full-length ratio at the 5′-end sequence of respective clones in thehuman cDNA libraries constructed by the oligo-capping method wasdetermined as follows. The clones whose 5′-end sequences were consistentwith those of known human mRNA in the public database were judged to be“full-length” if they had a longer 5′-end sequence than that of theknown human mRNA; or even though the 5′-end sequence was shorter, if itcontained the translation initiation codon it was judged to have the“full-length” sequence. Clones which did not contain the translationinitiation codon were judged to be “not-full-length”. The full-lengthratio ((the number of full-length clones)/(the number of full-length andnot-full-length clones)) at the 5′-end of the cDNA clones from eachlibrary was determined by comparing with known human mRNA. As a result,the full-length ratio of the 5′-ends was 63.5%. The result indicatesthat the full-length ratio at the 5′-end sequence was extremely high inthe human cDNA clones obtained by the oligo-capping method.

EXAMPLE 3 Assessment of the Full-Length Ratio of the 5′-End of the cDNAby the ATGpr and the ESTiMateFL

The ATGpr, developed by Salamov A. A., Nishikawa T., and Swindells M. B.in the Helix Research Institute, is a program for prediction of thetranslation initiation codon based on the characteristics of thesequences in the vicinity of the ATG codon (Salamov et al.,Bioinformatics 14:384-390, 1998; http://www.hri.co.jp/atgpr/). Theresults are shown with expectations (also mentioned as ATGpr1 below)whether the ATG is a true initiation codon (0.05-0.94). When the programwas applied to the 5′-end sequences of the clones from the cDNA librarythat was obtained by the oligo-capping method having 65% full-lengthratio, the sensitivity and specificity of the estimation of thefull-length clone (clone containing the N-terminus of the ORF) wereimproved to 82 to 83% by selecting only clones having an ATGpr1 score0.6 or higher. The maximum ATGpr1 score for 5′-end sequence ofNT2RP3001495 was 0.94.

Next, the ESTiMateFL was used for the assessment of the clones. TheESTiMateFL, developed by Nishikawa and Ota in the Helix ResearchInstitute, is a method for selecting clones expected to have afull-length cDNA by comparing with the 5′-end or 3′-end sequences ofESTs in the public database.

By this method, a cDNA clone is judged to be most likely not to befull-length if there exist any ESTs which have longer 5′-end or 3′-endsequences than the clone. The method is systematized for high throughputanalysis. A clone is judged to be full-length if the clone has a longer5′-end sequence than the ESTs in the public database correspondingthereto. Even if a clone has a shorter 5′-end, the clone is judged to befull-length if the difference in length is within 50 bases, andotherwise judged not to be full-length, for convenience. Those cloneswhose 5′-end sequence is matching with the known mRNA, about 80% of theclones judged to be full-length by the comparison with ESTs were alsojudged to be full-length by the assessment of the 5′-end sequence bycomparing with known mRNA. Also, about 80% of the clones judged to benot full-length in the 5′-end sequence by comparing with ESTs were alsojudged to be not full-length in the 5′-end sequence by comparison withknown mRNA. The precision of the estimation by comparing with ESTs isimproved with increasing numbers of ESTs to be compared. However, incase with limited numbers of ESTs, the reliability becomes low. Thus,the method is effective in excluding clones with high probability ofbeing not-full-length from the cDNA clones that is synthesized by theoligo-capping method having a 5′-end sequence full-length ratio of about60%. In particular, the ESTiMateFL is efficiently used in estimating thefull-length ratio at the 3′-end sequence of cDNA of a human unknownmRNA, a significant number of which are deposited in the public databaseas EST deposits.

Results of the above assessment for the full-length ratio showed thatthe clone NT2RP3001495, of which maximal value of ATGpr1 is greater than0.3, is a novel clone with a high probability of being full-length andalso which shares no sequence identity with any of human EST sequencesat least either at the 5′-end sequence or 3′-end sequence, or both ends.

EXAMPLE 4 Isolation of cDNA Associated with the Maintenance ofDifferentiation of Chicken Smooth Muscle Cells

New-laid eggs from chicken White Leghorn were incubated at 37° C. in anincubator. The fetuses were taken out after 15-day incubation. Thegizzard was resected and placed in a dish containing PBS (phosphatebuffer) with forceps. The resected gizzard was cut into small blockswith scissors, and then, was dispersed as individual cells bycollagenase treatment. Then, large cell aggregates were removed with afilter of 100 μm. The cells were washed with Dulbecco's modified Eagle'smedium (Nissui #05919) containing 20 mg/ml bovine serum albumin (BSA:SigmaA-7638), and the cell count was determined with a hemocytometer.5×10⁴ cells were plated on a 3.5-cm petri-dish, and were cultured at 37°C. overnight. These culture media were changed with 20 mg/ml BSA/DMEMcontaining 0.2 ng/ml insulin-like growth factor (IGF-I; BoehringerMannheim #1048066), and the media were replaced by fresh ones every twodays. The concentration of collagenase type-V (SigmaC-9263) was adjustedto 1 mg/ml by using Sol.3 (137 mM NaCl, 5 mM KCl, 4 mM NaHCO₃, 5.4 mMGlucose, 2 mM MgCl₂, 10 mM PIPES; adjusted to pH6.5), and thecollagenase solution was used after sterilization by filtration. On theninth day of culture the cells were harvested, and then the total RNAwas extracted therefrom. The cells cultured with culture mediumcontaining IGF-I are called differentiated smooth muscle cells in theexperiments described below, while the cells that had been changed tohave a proliferative character by adding bovine serum or anti-IGF-Iantibody (Upstate Biotechnology #05-172) at a concentration of 5 μg/ml,are called dedifferentiated smooth muscle cells. The cells were notdedifferentiated by the addition of mouse IgG antibodies (hereinafterreferred to as control antibodies), which were not the anti-IGF-Iantibody but the subclass of which were the same as that of theanti-IGF-I antibody, and thus, the cells were maintained as thedifferentiated smooth muscle cells. Complementary DNAs were synthesizedfrom 1 μg of the total RNAs extracted from differentiated cells ordedifferentiated cells of chicken smooth muscle that had been preparedby adding the control antibodies or anti-IGF-I antibodies. The synthesisof the cDNAs was carried out by a method using CapFinede PCR SynthesisKit (CLONTECH #K1052-1) according to the manual thereof. Specifically,total RNAs used were prepared from three types of cells: chicken gizzardsmooth muscle cells dedifferentiated by adding neutralizing anti-IGF-Iantibodies (hereinafter abbreviated as CGSMC-B); differentiated smoothmuscle cells by the addition of 0.2 ng/ml IGF-I and the controlantibodies (hereinafter abbreviated as CGSMC-C); and dedifferentiatedsmooth muscle cells obtained one day after the addition of bovine serum(hereinafter abbreviated as CGSMC-D). A 3.5 μl solution containing 1 μgof total RNA, 1 μl of CDS primer (attached to the kit) and 0.5 μl ofCapSwitch II oligo (attached to the kit) were mixed, incubated at 70° C.for 2 minutes, and then was allowed to stand at room temperature. Then,according to the manual attached to the kit, 2 μl of 5× first strandbuffer, 1 μl of DTT, 1 μl of 10 mM dNTP and 1 μl of MMLV reversetranscriptase were further added to the mixture, and the resultingmixture was incubated at 42° C. for 1 hour. 40 μl of TE (pH7.5) wasadded to the mixture, and then the resulting solution was incubated at72° C. for 7 minutes. A 1-μl aliquot of the resulting cDNA was diluted10-fold with distilled water, and was used for the PCR as describedbelow. The composition of the reaction mixture was as follows.

Composition of Reaction Mixture:

10 μl cDNA (10-fold dilution)

10 μl 10× Advantage KlenTaq buffer

4 μl 2.5 mM dNTP

2 μl 10 μM PCR primer (attached to the kit)

2 μl Advantage KlenTaq mix (50×)

72 μl distilled water

0.2-ml PCR tubes containing the above-mentioned reaction components wereplaced on a Thermal Cycler PE2400 (PE Biosystems) preheated to 95° C.After the denaturation at 95° C. for 1 minute, PCR was conducted with 15cycles of two steps: 95° C. for 15 seconds and then 68° C. for fiveminutes. Then, PCR was further continued with the same two-step profile,but a 15-μl aliquot was taken as a sample every 3 cycles. The sampleswere used to identify the number of cycles where the products by PCRamplification had been increased logarithmically and, at the same time,where the amplification had not been yet saturated. The results showedthat the condition of 17 cycles may be reasonable, and thus PCRamplification was conducted under this condition by using 8 tubes foreach cDNA. The product of the PCR amplification in 8 tubes for each cDNAwere combined together, and then, were deproteinized by mixing with anequal volume of phenol/chloroform/isoamyl alcohol (25:24:1). Then, thesolutions were concentrated by n-butanol extraction. The concentratedsolutions were subjected to CLONTECH CHROMA SPIN-1000 Column, and then,were eluted according to the manual by using 1×TNE buffer (10 mMTris-HCl (pH8.0)/10 mM NaCl/0.1 mM EDTA). The subtraction was carriedout using the resulting cDNA according to the manual of CLONTECHPCR-Select Subtraction Kit. 2 μg cDNA of CGSMC-B, CGSMC-C or CGSMC-D wasdigested with 15 units of restriction enzyme RsaI in a total solutionvolume of 50 μl by using a buffer attached to the kit at 37° C. for 3hours. 2.5 μl of 20×EDTA/glycogen mix attached to the kit and 3 volumesof SALT solution (attached to the kit) were added to the mixture. Theresulting mixture was vigorously mixed, and then 81 μl of PCR-Pure BIND(attached to the kit) was added thereto. The mixed solution wasincubated at room temperature for five minutes, and then centrifuged at14,000 rpm for one minute. The supernatant was removed, and theprecipitate was dissolved in 1 ml of WASH Solution (attached to the kit)by pipetting. The solution was again centrifuged at 14,000 rpm for oneminute, and the supernatant was removed. Further, the residual WASHSolution was removed completely by repeating centrifugation. Afterair-drying for 10 minutes, the precipitate was suspended in 17 μl of TEbuffer by pipetting, and then the suspension was incubated at roomtemperature for five minutes while keeping the suspended state of thesolution. Then, the solution was centrifuged at 14,0000 rpm for fiveminutes. The supernatant containing eluted DNA was transferred to aseparate tube, and then 9 μl of 4 M ammonium acetate (NH₄OAc; attachedto the kit) and 75 μl of ethanol were added thereto for ethanolprecipitation. The tube was centrifuged for 20 minutes, and theresulting precipitate was washed with 80% ethanol. The precipitate wasair-dried for 10 minutes, and then was dissolved in 6.7 μl of 1×TNEbuffer. The sample of CGSMC-C, RsaI-digested cDNAs of whichconcentration was adjusted to 300 ng/μl, was used a tester, andtherefore, the sample was further subjected to adapter ligation. Thesample of CGSMC-C was incubated for ligation with adapter 1 (10 μM) oradapter 2 (10 μM) (both attached to the kit) by using 1 μl of T4 DNAligase in a total volume of 10 μl containing Ligation buffer attached tothe kit at 16° C. overnight. 1 μl of 20×EDTA/glycogen mix was added tothe mixture, and then the enzyme was inactivated by the treatment at 72°C. for five minutes. The resulting adapter-ligated tester cDNAs arecalled TC-1 and TC-2, respectively.

1.5 μl of each dedifferentiated chicken gizzard smooth muscle cells,CGSMC-B and CGSMC-D (300 ng/μl), which serve as driver cDNA digestedwith restriction enzyme RsaI, were combined with 1.5 μl of TC-1 and 1.5μl of 4× Hybridization buffer attached to the kit to a total volume of 6μl in a 0.2-ml tube. Then, one drop of mineral oil was added thereto,and this is referred to as H1. Similarly, a tube was prepared with TC-2instead of TC-1, and was named H2. H1 and H2 were heated fordenaturation at 98° C. for 90 seconds in a Thermal cycler (PE BiosystemsPE2400), and then were incubated at 68° C. for 8 hours. A driver cDNAsolution with a total volume of 4 μl was freshly prepared by combining1.5 μl of dedifferentiated chicken gizzard smooth muscle cells, CGSMC-Band CGSMC-D (300 ng/μl), respectively, digested with restriction enzymeRsaI, and 1 μl of 4× Hybridization buffer attached to the kit. Thesolution was denatured by heat at 98° C. for 90 seconds. An air bubblewas sucked into the 200-11 pipette tip containing H2 to avoid directcontact of the solution with a solution of denatured driver cDNA thatwas sucked therein later. The solutions were transferred in a tubecontaining H1, and then were mixed by pipetting. The tube containing H1was allowed to stand on a Thermal cycler during the manipulation. Thetube was incubated at 68° C. overnight to hybridize the tester cDNA tothe cDNA in the driver cDNA. 200 μl of Dilution Buffer (attached to thekit) was added and mixed by pipetting, and the resulting mixture wasincubated at 75° C. for 7 minutes. This was stored as a dilutedsubtracted CGSMC IGF(+) cDNA at −20° C. The diluted subtracted CGSMCIGF(+) cDNA was subjected to primary PCR in a reaction solutioncontaining the following components.

Composition of Reaction Mixture:

 16 μl distilled water 2.5 μl 10x Advantage KlenTaq PCR buffer   4 μl2.5 mM dNTPs (TAKARA)   1 μl  10 μM PCR primer 1 (attached to the kit)0.5 μl 50x Advantage KlenTaq DNA polymerase   1 μl diluted subtractedCGSMC IGF(+) cDNA

These components were mixed in a 0.2-ml tube, and one drop of mineraloil was added thereto. After incubation at 75° C. for five minutes, andthen at 94° C. for 25 seconds, PCR was conducted with 27 cycles of threesteps: 94° C. for 10 seconds, 66° C. for 30 seconds, and 72° C. for 90seconds. 3 μl of the primary PCR product was diluted with 27 μl ofdistilled water, and then the following PCR was conducted.

Composition of Reaction Mixture:

18.5 μl distilled water  2.5 μl 10x Advantage KlenTaq PCR buffer  0.5 μl10 mM dNTPs (attached to the kit)   1 μl 10 μM Nested primer 1 (attachedto the kit)   1 μl 10 μM Nested primer 2 (attached to the kit)  0.5 μl50x Advantage KlenTaq DNA polymerase   1 μl 10 times diluted primary PCRproduct

These components were mixed in a 0.2-ml tube, and one drop of mineraloil was added thereto. After incubation at 94° C. for 25 seconds, PCRwas conducted with 19 cycles of three steps: 94° C. for 10 seconds, 66°C. for 30 seconds, and 72° C. for 90 seconds. A sample was taken fromthe tube at cycles 13, 15, 17, and 19, respectively, and then,amplification of PCR products were tested by agarose gelelectrophoresis. According to the result, the products seemed to besaturated with more than 15 cycles. Thus, products obtained with 15cycles of PCR were used to carry out the following experiment. 8 μl outof a total reaction volume of 25 μl was used in the electrophoresis, andthe remaining 17 μl was combined with 5 volumes of buffer PB (QIAGEN;buffer attached to Qiaquick PCR purification kit). The resultingsolution was mixed well. This was loaded onto Qiaquick column (acomponent of the same kit as described above), and the column wascentrifuged at 13,000 rpm. 7501 μl of Buffer PE (a component of the samekit as described above) was added to the column, and then the column wascentrifuged again. A fraction (5 μl) eluted with 30 μl of water attachedto the kit was used for TA cloning with a pGEM-T Vector system (A3600)from Promega according to the manual. After ligation at 4° C. overnight,2 μl of the reaction solution was used for the transformation of E. ColiDH5α according to the procedure of the kit. The resulting colonies wereused for colony PCR using the above-mentioned Nested primer 1 and Nestedprimer 2. The resulting PCR products were purified by using MultiScreenfrom Millipore to remove the primers. Then DNA sequence analysis wasperformed by using respective primers and the Dye Terminator CycleSequencing FS Ready Reaction kit (Perkin Elmer; Catalog #402122). Thenucleotide sequence of the resulting cDNA fragment was determined, and asequence named “12F08” (SEQ ID NO:3) was obtained.

EXAMPLE 5 Isolation of Human Novel Gene “C-NT2RP3001495” Having Homologyto Chicken “12F08”

NCBI UniGene database was searched for homology to the cDNA fragment“12F08” (SEQ ID NO:3) obtained in Example 4 by NCBI BLASTN2.0. Theresult showed that the “12F08” sequence exhibited 82% homology to aclone Hs#S1388556 belonging to human Unigene cluster Hs.128045.Considering that the sequence comparison was made between chicken andhuman, the gene belonging to Unigene cluster Hs.128045 can be concludedto be the human orthologue to chicken 12F08. Then, the followingsequences belonging to Hs.128045 were assembled into a contig, and theobtained sequence was named Hs128045_(—)12F08con.

-   gnl|UG|Hs#S1388556 wb85d11.x1 Homo sapiens cDNA, 3′    end/clone=IMAGE:2312469/clone_end=3′/gb=AI669330/gi=4834104-   gnl|UG|Hs#S1579061 wr85e01.x1 Homo sapiens cDNA, 3′    end/clone=IMAGE:2494488/clone_end=3′/gb=AI984802/gi=5812079-   gnl|UG|Hs#S 1008273 op61g03.s1 Homo sapiens cDNA, 3′    end/clone=IMAGE: 1581364/clone_end=3′/gb=AA970231/gi=3145744-   gnl|UG|Hs#S984806 o141b06.s1 Homo sapiens cDNA, 3′    end/clone=IMAGE:1526003/clone_end=3′/gb=AA912726/gi=3052118

The pfam motif database was searched for Hs128045_(—)12F08con usingestwisedb of the database search programs Wise2 designed by Ewan Birneyat Sanger Center. The result showed that both 12F08 andHs128045_(—)12F08con contained two WW domains. The WW domain is known tobe an important functional domain for protein-protein interaction, andmany proteins containing WW domain have been reported.

Then, cDNA sequences of the Helix Research Institute (helix clones;Japanese Patent Application No. Hei 11-248036; Japanese PatentApplication No. 2000-118776) were searched using the sequence obtainedfrom the above-mentioned Unigene Cluster as a query. The cDNA sequencesof the Helix Research Institute are clones obtained by the method inExamples 1 to 3 which probability of containing a full-length sequenceis high.

The homology search using the helix clones revealed that the sequencewas identical to that of a helix clone “C-NT2RP3001495”. In addition,the gene has been identified to be identical to Hs.519 Humanoxidoreductase (HHCMA56) of Unigene as well. However, detailed analysisby using GAP of GCG Packaging software showed that “C-NT2RP3001495” waslonger than HHCMA56; the sequence of HHCMA56 started at nucleotide 578of “C-NT2RP3001495” sequence; the C-residue triplet at nucleotides 276to 278 in the sequence of HHCMA56 was altered to a C-residue doublet inthe sequence of “C-NT2RP3001495”; and further, the G-residue triplet atnucleotides 280 to 282 in the sequence of HHCMA56 was altered to aG-residue doublet at nucleotides 856 to 858 in the sequence of“C-NT2RP3001495”. Therefore, PCR amplification was performed using theoligonucleotide, 1495-588U24 (5′-GCA GGA ACA TGG CAA GGG CGA GTG-3′/SEQID NO:9), corresponding to the 24 nucleotides starting from nucleotide588 of “C-NT2RP3001495”, and the oligonucleotide, 1495-862L23 (5′-GGGCAG GAG CTG AGC GGC ACA AA-3′/SEQ ID NO:10), having a complementarystrand to the 23 nucleotides starting from nucleotide 839 of“C-NT2RP3001495”, as well as human genomic DNA (Clontech #6550-1) as thetemplate (pre-heating at 94° C. for 5 minutes; 45 cycles of denaturationat 94° C. for 15 seconds, annealing at 55° C. for 30 seconds, andextension at 72° C. for 30 seconds; final extension at 72° C. for 3minutes). The resulting DNA was cloned into pGEM-T (Promega; A3600), andthe sequence was determined.

As a result, it was revealed that the sequence of “C-NT2RP3001495” wascorrect, and the sequence of HHCMA56 contained incorrect nucleotides bymisreading. Positional relation between the amino sequences encoded byrespective genes is shown in FIG. 1. While an adh short motif, which isa motif found in oxidoreductase and dehydrase, is present in HHCMA56,the two WW domains, which are present in “C-NT2RP3001495”, are not foundin HHCMA56. In addition, because of two nucleotide differences, HHCMA56has been deposited as a gene encoding a protein consisting of 371 aminoacids, which is entirely different from “C-NT2RP3001495”. Thus, it canbe stated that “C-NT2RP3001495” is a novel protein found for the firsttime by the present inventors. The protein “C-NT2RP3001495” is a proteinconsisting of 414 amino acids which contains two WW domain sequences,and is associated with the maintenance of differentiation of smoothmuscle cells.

Furthermore, after the identification of the novel protein“C-NT2RP3001495” by the present inventors, a result of homology searchby BLASTN revealed that the sequence was identical to that depositedunder an accession number AF211943 (submitted on Dec. 7, 1999; publishedon May 5, 2000) in GenBank by Bednarek A K et al. (University of TexasMD Anderson Cancer Center). (WWOX, a novel WW domain-containing proteinmapping to human chromosome 16q23.3-24.1, a region frequently affectedin breast cancer, Cancer Res. 60(8): 2140-2145, 2000).

EXAMPLE 6 Expression Analysis of Chicken “12F08”

The expression level of the gene, chicken “12F08”, was analyzed byreal-time PCR using ABI PRISM(R) 7700 Sequence Detection System from PEBiosystems (PCR Meth. And Appl. 4:357-362, 1995). By usingoligonucleotides of sequence 8 (5′-GGT GGC TTT GCT GGA TTA TCT T-3′/SEQID NO:11) and sequence 9 (5′-GTT GCA GGA GGT CTG CCA TAT G-3′/SEQ IDNO:12), as well as G3PDH as an indicator, the expression levels of themRNA were compared with one another among chicken aorta (Ao), AoSMC cellderived from the aorta (AoDD), A (differentiated primary culture cell ofchicken gizzard smooth muscle), B (dedifferentiated primary culture cellof chicken gizzard smooth muscle by the addition of anti-IGF-Iantibody), C (differentiated primary culture cell of chicken gizzardsmooth muscle by the addition of control antibody), F1 (dedifferentiatedprimary culture cell of chicken gizzard smooth muscle one day after theaddition of FCS), Br (brain), Ca (cardiac muscle), Gz (gizzard), and Lv(liver). The total RNAs, which had been extracted from chicken tissuesof aorta (Ao). Br, Ca, Gz, and Lv directly obtained from a chicken, werekindly provided by Dr. Sobue at Osaka University. CAOMC (TC354-05) fromCell Applications, Inc. had been purchased from Toyobo. These cells werecultured according to the instructions in the protocol, and were used asAoSMC (AoDD) cells.

The results of real-time RT-PCR with AB17700 are shown in Table 1. PCRwas carried out with pre-heating at 95° C. for 10 minutes, and 50 cyclesof denaturation at 94° C. for 20 seconds, annealing at 55° C. for 20seconds, and extension at 72° C. for 30 seconds by using SYBR Green PCRCore Reagent kit (PE Biosystems; 4304886). Each value is obtained bydividing the value of 12F08 expression level by the value of expressionlevel of G3PDH as a control. The greater the value is, the higher theexpression level of 12F08 gene in the cells will be. The chicken “12F08”was found to be expressed at a high level in differentiated smoothmuscle and gizzard. Accordingly, it was suggested that the chicken“12F08” gene encodes a protein participating in the maintenance ofdifferentiation of smooth muscle cells.

TABLE 1 Tissue Cells mRNA expression amount Ao 17.14 AoDD 0.88 A 3.43 B2.37 C 8.4 Fl 2.18 Br 4.45 Ca 2.36 Gz 6.41 Lv 1.35

EXAMPLE 7 Gene Expression Analysis by Hybridization Using High DensityDNA Filter

DNA for spotting onto the nylon membranes was prepared according to thefollowing procedure. E. coli was cultured in each well of a 96-wellplate (in a LB medium at 37° C. for 16 hours). A part of each culturewas suspended in 10 μl of sterile water in the well of a 96-well plate.The plate was heated at 100° C. for 10 minutes. Then the samples wereanalyzed by PCR. PCR was performed in a 20 μl solution per one reactionby using TaKaRa PCR Amplification Kit (Takara) according to thesupplier's protocol. A pair of sequencing primers, ME761 FW (5′tacggaagtgttacttctgc 3′/SEQ ID NO:13) and ME1250RV (5′tgtgggaggttttttctcta 3′/SEQ ID NO:14), or a pair of primers, M13M4 (5′gttttcccagtcacgac 3′/SEQ ID NO:15) and M13RV (5′ caggaaacagctatgac3′/SEQ ID NO:16) were used for the amplification of the insert cDNA inthe plasmid. PCR was performed in a thermal cycler, GeneAmp System 9600(PE Biosystems). The cycling profile consisted of pre-heating at 95° C.for 5 minutes; 10 cycles of denaturation at 95° C. for 10 seconds, andannealing/extension at 68° C. for 1 minute; 20 cycles of denaturation at98° C. for 20 seconds and annealing/extension at 60° C. for 3 minutes;and final extension at 72° for 10 minutes. After the PCR, 2 μl of thereaction solution was electrophoresed on a 1% agarose gel. DNA on thegel was stained with ethidium bromide to confirm the amplification ofcDNA. When cDNAs were not amplified by PCR, plasmids containing thecorresponding insert cDNAs were prepared by the alkali-extraction method(Sambrook et al., Molecular Cloning, A laboratory manual/2nd edition,Cold Spring Harbor Laboratory Press, 1989).

DNA array was prepared by the following procedure. An Aliquot of the DNAsolution was added to each well of a 384-well plate. DNA was spottedonto a nylon membrane (Boehringer) by using a 384-pin tool of Biomek2000 Laboratory Automation System (Beckman-Coulter). More specifically,the 384-well plate containing the DNA was placed under the 384-pin tool.The independent 384 needles of the pin tool were simultaneously dippedinto the DNA solution to fix the DNA on the needles. The needles weregently pressed onto a nylon membrane, and the DNA fixed on the needleswas spotted onto the membrane. Denaturation of the spotted DNA andimmobilization of the DNA on the nylon membrane were carried outaccording to conventional methods (Sambrook et al., Molecular Cloning, Alaboratory manual/2nd edition, Cold Spring Harbor Laboratory Press,1989).

1st strand cDNA labeled with radioisotope was used as the hybridizationprobe. The 1st strand cDNA was synthesized by using Thermoscript™ RT-PCRSystem (GIBCO). More specifically, the 1st strand cDNA was synthesizedby using 1.5 μg mRNAs from various human tissues (Clontech), 1 μl 50 μMOligo(dT)20, and 50 μCi [α³³P]dATP according to the attached protocol.Purification of the probe was carried out by using ProbeQuant™ G-50micro column (Amersham-Pharmacia Biotech) according to the attachedprotocol. In the next step, 2 units of E. coli RNaseH were added to thereaction mixture. The mixture was incubated at room temperature for 10minutes, and then 100 μg of human COT-1 DNA (GIBCO) was added thereto.The mixture was incubated at 97° C. for 10 minutes, and then was allowedto stand on ice to give the hybridization probe.

Hybridization of the radioisotope-labeled probe to the DNA array wasperformed in a usual manner (Sambrook et al., Molecular Cloning, Alaboratory manual/2nd edition, Cold Spring Harbor Laboratory Press,1989). The membrane was washed as follows: the nylon membrane was washedthree times by incubating in the Washing solution 1 (2×SSC, 1% SDS) atroom temperature (about 26° C.) for 20 minutes; then the membrane waswashed 3 times by incubating it in the Washing solution 2 (0.1×SSC, 1%SDS) at 65° C. for 20 minutes. Autoradiography was performed by using animage plate for BAS2000 (Fuji Photo Film Co., Ltd.). Specifically, thenylon membrane used for the hybridization was wrapped with a piece ofSaran Wrap, and was contacted with the light-sensitive surface of theimage plate. The membrane with the image plate was placed in an imagingcassette for radioisotope and was allowed to stand in dark for 4 hours.The radioactivity recorded on the image plate was analyzed by BAS2000(Fuji Photo Film Co., Ltd.) and was recorded as an image file of theautoradiogram by electronic conversion. The signal intensity of each DNAspot was analyzed by using Visage High Density Grid Analysis Systems(Genomic Solutions Inc.). The signal intensity was converted intonumerical data. The data were taken by duplicated measurements. Thereproducibility was assessed by comparing the signal intensities of thecorresponding spots on the duplicated DNA filters that were hybridizedto a single DNA probe. The ratio between the corresponding spots fallswithin a range of 2-folds or less in 95% of entire spots, and thecorrelation coefficient was r=0.97. Thus, the reproducibility wasassumed to be satisfactory.

The detection sensitivity in gene expression analysis was estimated byexamining increases in the signal intensity of the probeconcentration-dependent spot of the hybridization using a probecomplementary to the DNA spotted on the nylon membrane. PLACE1008092(the same DNA as that deposited in GenBank Accession No. AF107253) wasused as the DNA. The DNA array with the DNA of PLACE1008092 was preparedaccording to the above-mentioned method. The probe was prepared asfollows: mRNA was synthesized in vitro from the clone, PLACE1008092;using this mRNA as the template, radioisotope-labeled 1st strand cDNAwas synthesized in the same manner as the probe preparation methoddescribed above; and the cDNA was used as the probe. The cDNAPLACE1008092 was inserted into pBluescript SK(−), so that the 5′-end ofthe PLACE1008092 is ligated to the T7 promoter of the pBluescript SK(−)to give a recombinant plasmid for in vitro synthesis of the mRNA fromPLACE1008092. Specifically, the PLACE1008092 inserted at the DraI siteof the pME18SFL3 was cut out by XhoI digestion. The resultingPLACE1008092 fragment was ligated to XhoI-predigested pBluescript SK(−)by using the DNA ligation kit ver.2 (Takara). The in-vitro mRNAsynthesis from PLACE1008092 inserted in pBluescript SK(−) was carriedout by using the Ampliscribe™ T7 high yield transcription kit (Epicentretechnologies). The hybridization and analysis of signal intensity ofeach DNA spot were conducted using the same methods described above.When the probe concentration was 1×10⁷ μg/ml or less, there was noincrease of signal intensity proportional to the probe concentration.Therefore it was assumed to be difficult to compare the signals with oneanother in this concentration range. Thus, spots with a intensity of 40or less were indiscriminately taken as low-level signals (FIG. 3).Within a concentration of the probe ranging from 1×10⁷ μg/ml to 0.1μg/ml, signals were found to increase in a probe concentration-dependentmanner. The detection sensitivity is 1:100,000 in a ratio of mRNAexpression level in a sample.

Table 2 shows the expression of each cDNA in human normal tissues(heart, lung, pituitary gland, thymus, brain, kidney, liver and spleen).The expression levels are indicated by numerical values of 0 to 10,000.The “C-NT2RP3001495” was expressed in at least one tissue.

TABLE 2 Clone Pituitary name Heart Lung gland Thymus Brain Kidney LiverSpleen GAPDH 38.210 32.670 23.820 13.580 11.230 21.120 24.910 22.440β-actin 279.280 368.870 111.100 117.500 92.880 114.650 82.990 256.790NT2RP3001495 42.340 19.294 36.741 7.565 17.241 28.985 27.157 19.314

EXAMPLE 8 Analysis of Genes Associated with Neural Cell Differentiation

Genes involved in neural cell differentiation are useful for treatingneurological diseases. It is possible that genes with varying expressionlevels in response to induction of cellular differentiation in neuralcells are associated with neurological diseases. It was examined whetherthe expression of “C-NT2RP3001495” varies in response to induction ofdifferentiation (stimulation by retinoic acid (RA)) in cultured cells ofa neural strain, NT2.

The NT2 cells were treated basically according to the supplier'sinstruction manual. The term “undifferentiated NT2 cells” refers to NT2cells successively cultured in an OPTI-MEM 1 (GIBCO BRL; catalog No.31985) containing 10%(v/v) fetal bovine serum (GIBCO BRL) and 1%(v/v)penicillin-streptomycin (GIBCO BRL). The term “NT2 cells cultured in thepresence of retinoic acid” refers to cells passaged for 5 weeksfollowing transferring of the undifferentiated NT2 cells into a retinoicacid-containing medium, which consists of D-MEM (GIBCO BRL; catalog No.11965), 10%(v/v) fetal bovine serum, 1%(v/v) penicillin-streptomycin and10 μM retinoic acid (GIBCO BRL). The term “NT2 cells that were culturedin the presence of retinoic acid, and which were further cultured in amedia with the addition of cell-division inhibitor” refers to NT2 cellspassaged for 2 weeks following transferring of the NT2 cells cultured inthe presence of retinoic acid for 5 weeks into a cell-divisioninhibitor-containing medium, which consisted of D-MEM (GIBCO BRL;catalog No. 11965), 10%(v/v) fetal bovine serum, 1%(v/v)penicillin-streptomycin, 10 μM retinoic acid, 10 μM FudR(5-fluoro-2′-deoxyuridine: GIBCO BRL), 10 μM Urd (Uridine: GIBCO BRL)and 11M araC (Cytosine β-D-Arabinofuranoside: GIBCO BRL). Each of thecells were treated with trypsin and then were harvested. Total RNAs wereextracted from the cells by using S.N.A.P.™ Total RNA Isolation kit(Invitrogen). The probe used for hybridization was labeled by using 10μg of the total RNA according to the same methods as described above.

The data were obtained in triplicate (n=3). The data of signal valuerepresenting gene expression level in the cells in the presence ofstimulation for inducing differentiation were compared with thosewithout the stimulation. The comparison was performed by statisticaltreatment of two-sample t-test. Clones with significant difference inthe signal distribution were selected under the condition of p<0.05. Inthis analysis, clones with difference can be statistically detected evenwhen the signals are low. Accordingly, clones with signal value of 40 orless were also assessed.

Table 3 shows the expression level of “C-NT2RP3001495” cDNA inundifferentiated NT2 cells. NT2 cells cultured in the presence of RA,and NT2 cells cultured with the addition of cell-division inhibitorafter culturing in the presence of RA.

Averaged signal values (M₁, M₂) and sample variances (s₁ ², s₂ ²) werecalculated for each gene in each of the cells, and then, the pooledsample variances s² were obtained from the sample variances of the twotypes of cells to be compared. The t values were determined according tothe following formula: t=(M₁−M₂)/s/(⅓+⅓)^(1/2). When the determinedt-value was grea a t-value at P, the probability of significance level,of 0.05 or 0.01 in the t-distribution table with 4 degrees of freeedom,it was judged there exists a difference in the expression level of thegenes between the two types of cells at P<0.05 or P<0.01, respectively.The table also includes the information on an increase (+) or decrease(−) in the average expression level of a signal in the clones comparedwith that of undifferentiated cells.

As a result, the expression of the “C-NT2RP3001495” was shown toincrease by RA, suggesting that it is a clone involved in neurologicaldisorders.

TABLE 3 NT2 NT2 RA NT2 RA INHIB ttest + ttest + Clone exp. 1 exp. 2 exp.3 exp. 1 exp. 2 exp. 3 exp. 1 exp. 2 exp. 3 N/R − N/I − GAPDH(C21) 3.531.06 0.98 2.93 2.49 2.8 1.76 2.59 1.52 β actin(Cr2) 155.38 1.18 99.68148.45 110.68 101.34 114.68 105.79 151.13 NT2RP3001495 4.27 2.41 2.484.72 5.59 4.95 3.72 4.06 3.66 * +

EXAMPLE 9 Analysis of Rheumatoid Arthritis-Associated Genes

Proliferation of synovial cells covering inner surfaces of joint cavityand inflammatory reaction resulted from the action of cytokines producedby leukocytes infiltrating into the joint synovial tissues is thought tobe involved in the onset of rheumatoid arthritis (Japan RheumatismFoundation Information Center, http://www.rheuma-net.or.jp/). Recentstudies have also revealed that tissue necrosis factor (TNF)-αparticipates in the onset of rheumatoid arthritis (Current opinion inimmunology 1999, 11, 657-662). Those genes whose expression levelchanges in response to the action of TNF on synovial cells areconsidered to be involved in rheumatoid arthritis. It was examinedwhether the expression of “C-NT2RP3001495” varies in response to TNF-αin the primary cell culture of synovial tissue.

The primary cultured synovial cells (Cell Applications) were grown to beconfluent in a culture dish, and then, human TNF-α (Boehringer-Mannheim)was added at a final concentration of 10 ng/ml thereto. The culture wasfurther continued for 24 hours. Total RNA was extracted from the cellsby using S.N.A.P.™ Total RNA Isolation kit (Invitrogen). The labeling ofthe probe used for hybridization was carried out by using 10 μg of thetotal RNA according to the same methods as described above. The datawere obtained in triplicate (n=3). The data of signal value representinggene expression level in cells with TNF stimulation were compared withthose without the stimulation. The comparison was performed bystatistical treatment of two-sample 1-test. Clones with significantdifference in the signal distribution were selected under the conditionof p<0.05. According to the analysis, clones with difference can bestatistically detected even when the signals were low. Accordingly,clones with signal value of 40 or less were also assessed for theselection.

Table 4 shows the expression level of each cDNA in synovial cellscultured under the absence or presence of TNF. Averaged signal values(M₁, M₂) and sample variances (s₁ ², s₂ ²) for each gene were calculatedin each of the cells, and then, the pooled sample variances s² wereobtained from the sample variances of the two types of cells to becompared. The t-values were determined according to the followingformula: t=(M₁−M₂)/s/(⅓+⅓)^(1/2). When the det t-value was greater thana t-value at P, probability of significance level, of 0.05 or 0.01 inthe 1-distribution table with 4 degrees of freedom, it was judged that adifference exists in the expression level of the gene between the twotypes of cells at P<0.05 or P<0.01, respectively. The table alsoincludes the information of an increase (+) or decrease (−) in theaverage expression level of a signal in the clones compared with that ofundifferentiated cells.

The results showed that the expression level of “C-NT2RP3001495” wasreduced by TNF-α, suggesting that it is a clone associated withRheumatoid arthritis.

TABLE 4 t test Synoviocyte Synoviocute_TNF vs + Clone exp. 1 exp. 2 exp.3 exp. 1 exp. 2 exp. 3 TNF − GAPDH(Cr1) 0.4 0.8 0.89 0.9 1 1.15 βactin(Cr2) 385.94 262.23 582.98 443.28 422.61 573.47 NT2RP3001495 4.144.14 3.85 2.75 2.92 1.76 * −

EXAMPLE 10 Analysis of Ultraviolet Radiation Damage-Associated Genes

It is known that ultraviolet rays give considerably adverse influence onhealth. In recent years, the risks of tissue damage by ultraviolet rayshas been increased due to the destruction of the ozone layer, andultraviolet radiation has been recognized as a risk factor for diseasessuch as skin cancers (United States Environmental Protection Agency:Ozone Depletion Home Page, http://www.epa.gov/ozone/). Genes whoseexpression levels change with exposure of the skin epidermal cells toultraviolet rays are considered to be associated with skin damage causedby ultraviolet radiation. Culturing primary cultured skin fibroblastcells irradiated with ultraviolet ray, it was examined whether theexpression of “C-NT2RP3001495” varies depending on the irradiation ofultraviolet ray.

First, after culturing to confluence in a culture dish, the primarycultured skin fibroblast cells (Cell Applications) were exposed to10,000 μJ/cm² of 254-nm ultraviolet light. Thereafter, messenger RNAswere extracted by using a FastTrack™ 2.0 mRNA Isolation kit (Invitrogen)from the unexposed cells and from the cells that were exposed to theultraviolet light and then cultured for 4 or 24 hours. The labeling ofthe hybridization probe was carried out by using 1.5 μg of each mRNA inthe same manner as described above. The data were obtained in triplicate(n=3). The hybridization signals were compared between the cells exposedto the ultraviolet light and the unexposed cells. The comparison waspreformed by statistical treatment with two-sample t-test. Clones withsignificant differences in the signal distribution were selected underthe condition of p<0.05. According to the analysis, the difference inthe signal values can be also detected statistically even when thesignal values are low. Accordingly, clones with signal value of 40 orlower were also assessed.

Table 5 shows the expression of each cDNA in skin-derived fibroblastcells exposed and unexposed to ultraviolet light.

Averaged signal values (M₁, M₂) and sample variances (s₁ ², s₂ ²) werecalculated for each gene in each of the cells, and then, pooled samplevariances s² were obtained from the sample variances of the two types ofcells to be compared. The t values were determined according to thefollowing formula: t=(M₁−M₂)/s/(⅓+⅓)^(1/2). When the determined t-valuewas grea a t-value at P, probability of significance level, of 0.05 or0.01 in the t-distribution table with 4 degrees of freedom, it wasjudged that a difference exists in the expression level of the genebetween the two types of cells at P<0.05 or P<0.01, respectively. Thetable also includes the information of an increase (+) or decrease (−)in the average expression level of a signal in the clones compared withthat of undifferentiated cells.

The results showed that the expression level of “C-NT2RP3001495” wasreduced 4 hours or 24 hours after ultraviolet ray irradiation,suggesting that it is a clone associated with ultraviolet ray disorders.

TABLE 5 UV_0 h UV_4 h UV_24 h t test 4 h 24 h Clone Exp. 1 Exp. 2 Exp. 3Exp. 1 Exp. 2 Exp. 3 Exp. 1 Exp. 2 Exp. 3 0/4 0/24 +/− +/− GAPDH(Cr1) 01.29 0.1 0.9 0.06 1.18 1.49 0.47 0 β actin(Cr2) 256.82 283.53 414.29388.38 117.29 329.8 189.18 190.26 157.87 * − NT2RP3001495 18.56 21.1119.03 12.08 9.76 9.93 15.89 18.33 21.35 ** −

INDUSTRIAL APPLICABILITY

The present invention provides a novel human protein “C-NT2RP3001495”associated with the maintenance of differentiation of smooth musclecells and the gene encoding the protein. The protein has two WW domainsthat participate in protein-protein interaction. Thus, it is presumedthat the protein regulates intracellular signal transduction, geneexpression and others through binding with other proteins, and therebyparticipates in the maintenance of differentiation of smooth musclecells. Abnormalities in the maintenance of differentiation of smoothmuscle cells have been known to cause a variety of diseases. Forexample, phenotypic modulation of vascular tunica media smooth musclecell to a dedifferentiated type is recognized in the early phases of theonset of arteriosclerosis and is known as the major cause of thickeningof vascular endothelium. Thus, the protein of the present inventionparticipating in the maintenance of differentiation of smooth musclecells is considered to play important roles in living body, andaccordingly, it is useful as a target molecule in drug development.Further, compounds controlling functions of the inventive protein areexpected to be pharmaceuticals for a variety of diseases caused by theabnormality in the maintenance of differentiation of smooth musclecells, for example, ischemic heart diseases such as arteriosclerosis,myocardial infarction, aortic aneurysm, and cerebral apoplexy; cerebralvascular disorders; vascular dementia; as well as glomerulonephritis,pulmonary fibrosis, cerebral arteriosclerosis, hepatitis, and such, thatare states of aberrant proliferation of mesangial cells, alveolarepithelial cells, pericytes, and lto cells, cells which have extremelysimilar characteristics to those of the smooth muscle cell.

What is claimed is:
 1. A substantially purified polypeptide comprising the amino acid sequence of SEQ ID NO:2.
 2. A substantially purified polypeptide comprising the amino acid sequence of SEQ ID NO:2 or a fragment thereof having the function of maintaining smooth muscle cells as differentiated cells.
 3. The polypeptide of claim 1 consisting of the amino acid sequence of SEQ ID NO:2.
 4. A substantially purified polypeptide that comprises the amino acid sequence of SEQ ID NO:2 in which up to 10 amino acids are replaced, deleted, and/or inserted, wherein said polypeptide has the function of maintaining smooth muscle cells as differentiated cells.
 5. The polypeptide of claim 4, wherein the number of amino acids that are replaced, deleted and/or inserted is up to
 5. 6. A substantially purified polypeptide encoded by a nucleic acid that hybridizes after washing with 0.1×SSC and 0.1% SDS at 65° C. with a probe consisting of the complete complement of the coding region of SEQ ID NO:1, wherein the polypeptide has the function of maintaining smooth muscle cells as differentiated cells.
 7. A substantially purified polypeptide that comprises an amino acid sequence at least 95% identical to SEQ ID NO:2, wherein the polypeptide has the function of maintaining smooth muscle cells as differentiated cells.
 8. The polypeptide of claim 7, wherein the amino acid sequence is at least 98% identical to SEQ ID NO:2. 